"Why? Shouldn't they be the same?"
Nothing in your question explains why different data should be visualised the same.
M2 = load('pp_Region2.mat').pp_Region2
M2 = 500×1000
    0.7954    0.7954    0.7951    0.7947    0.7941    0.7934    0.7925    0.7915    0.7903    0.7889    0.7874    0.7857    0.7839    0.7819    0.7797    0.7774    0.7750    0.7724    0.7696    0.7667    0.7637    0.7605    0.7572    0.7537    0.7501    0.7463    0.7425    0.7385    0.7343    0.7301
    0.7952    0.7951    0.7948    0.7944    0.7939    0.7931    0.7923    0.7912    0.7900    0.7886    0.7871    0.7854    0.7836    0.7816    0.7795    0.7772    0.7747    0.7721    0.7694    0.7665    0.7634    0.7603    0.7569    0.7535    0.7499    0.7462    0.7423    0.7383    0.7342    0.7299
    0.7949    0.7948    0.7946    0.7942    0.7936    0.7929    0.7920    0.7909    0.7897    0.7884    0.7868    0.7852    0.7833    0.7813    0.7792    0.7769    0.7745    0.7719    0.7691    0.7663    0.7632    0.7600    0.7567    0.7533    0.7497    0.7460    0.7421    0.7381    0.7340    0.7298
    0.7946    0.7945    0.7943    0.7939    0.7933    0.7926    0.7917    0.7907    0.7895    0.7881    0.7866    0.7849    0.7831    0.7811    0.7790    0.7767    0.7742    0.7716    0.7689    0.7660    0.7630    0.7598    0.7565    0.7531    0.7495    0.7458    0.7419    0.7380    0.7338    0.7296
    0.7943    0.7942    0.7940    0.7936    0.7930    0.7923    0.7914    0.7904    0.7892    0.7878    0.7863    0.7846    0.7828    0.7808    0.7787    0.7764    0.7740    0.7714    0.7687    0.7658    0.7628    0.7596    0.7563    0.7529    0.7493    0.7456    0.7417    0.7378    0.7337    0.7295
    0.7940    0.7940    0.7937    0.7933    0.7928    0.7920    0.7912    0.7901    0.7889    0.7876    0.7860    0.7844    0.7826    0.7806    0.7785    0.7762    0.7737    0.7712    0.7684    0.7656    0.7626    0.7594    0.7561    0.7527    0.7491    0.7454    0.7416    0.7376    0.7335    0.7293
    0.7938    0.7937    0.7934    0.7930    0.7925    0.7918    0.7909    0.7898    0.7886    0.7873    0.7858    0.7841    0.7823    0.7803    0.7782    0.7759    0.7735    0.7709    0.7682    0.7653    0.7623    0.7592    0.7559    0.7525    0.7489    0.7452    0.7414    0.7374    0.7333    0.7291
    0.7935    0.7934    0.7932    0.7928    0.7922    0.7915    0.7906    0.7896    0.7884    0.7870    0.7855    0.7839    0.7820    0.7801    0.7780    0.7757    0.7733    0.7707    0.7680    0.7651    0.7621    0.7590    0.7557    0.7523    0.7487    0.7450    0.7412    0.7373    0.7332    0.7290
    0.7932    0.7931    0.7929    0.7925    0.7919    0.7912    0.7903    0.7893    0.7881    0.7868    0.7853    0.7836    0.7818    0.7798    0.7777    0.7754    0.7730    0.7705    0.7677    0.7649    0.7619    0.7588    0.7555    0.7521    0.7485    0.7448    0.7410    0.7371    0.7330    0.7288
    0.7929    0.7928    0.7926    0.7922    0.7916    0.7909    0.7901    0.7890    0.7878    0.7865    0.7850    0.7833    0.7815    0.7796    0.7775    0.7752    0.7728    0.7702    0.7675    0.7647    0.7617    0.7585    0.7553    0.7519    0.7483    0.7446    0.7408    0.7369    0.7328    0.7287
<mw-icon class=""></mw-icon>
<mw-icon class=""></mw-icon>
M3 = load('pp_Region3.mat').pp_Region3
M3 = 500×1000
    0.6651    0.6650    0.6649    0.6647    0.6645    0.6642    0.6638    0.6633    0.6628    0.6622    0.6616    0.6608    0.6600    0.6592    0.6582    0.6572    0.6561    0.6550    0.6538    0.6525    0.6512    0.6498    0.6483    0.6468    0.6452    0.6435    0.6418    0.6400    0.6381    0.6362
    0.6649    0.6649    0.6648    0.6646    0.6644    0.6641    0.6637    0.6632    0.6627    0.6621    0.6614    0.6607    0.6599    0.6591    0.6581    0.6571    0.6560    0.6549    0.6537    0.6524    0.6511    0.6497    0.6482    0.6467    0.6451    0.6434    0.6417    0.6399    0.6381    0.6362
    0.6648    0.6648    0.6647    0.6645    0.6642    0.6639    0.6636    0.6631    0.6626    0.6620    0.6613    0.6606    0.6598    0.6589    0.6580    0.6570    0.6560    0.6548    0.6536    0.6524    0.6510    0.6496    0.6482    0.6466    0.6450    0.6434    0.6417    0.6399    0.6381    0.6362
    0.6647    0.6646    0.6645    0.6644    0.6641    0.6638    0.6634    0.6630    0.6625    0.6619    0.6612    0.6605    0.6597    0.6588    0.6579    0.6569    0.6559    0.6547    0.6535    0.6523    0.6509    0.6496    0.6481    0.6466    0.6450    0.6433    0.6416    0.6399    0.6380    0.6361
    0.6645    0.6645    0.6644    0.6642    0.6640    0.6637    0.6633    0.6629    0.6623    0.6618    0.6611    0.6604    0.6596    0.6587    0.6578    0.6568    0.6558    0.6546    0.6534    0.6522    0.6509    0.6495    0.6480    0.6465    0.6449    0.6433    0.6416    0.6398    0.6380    0.6361
    0.6644    0.6644    0.6643    0.6641    0.6639    0.6636    0.6632    0.6627    0.6622    0.6616    0.6610    0.6603    0.6595    0.6586    0.6577    0.6567    0.6557    0.6545    0.6534    0.6521    0.6508    0.6494    0.6480    0.6464    0.6449    0.6432    0.6415    0.6398    0.6379    0.6361
    0.6643    0.6643    0.6642    0.6640    0.6637    0.6634    0.6631    0.6626    0.6621    0.6615    0.6609    0.6602    0.6594    0.6585    0.6576    0.6566    0.6556    0.6544    0.6533    0.6520    0.6507    0.6493    0.6479    0.6464    0.6448    0.6432    0.6415    0.6397    0.6379    0.6360
    0.6642    0.6641    0.6640    0.6639    0.6636    0.6633    0.6629    0.6625    0.6620    0.6614    0.6608    0.6600    0.6593    0.6584    0.6575    0.6565    0.6555    0.6543    0.6532    0.6519    0.6506    0.6492    0.6478    0.6463    0.6447    0.6431    0.6414    0.6397    0.6379    0.6360
    0.6640    0.6640    0.6639    0.6637    0.6635    0.6632    0.6628    0.6624    0.6619    0.6613    0.6606    0.6599    0.6591    0.6583    0.6574    0.6564    0.6554    0.6543    0.6531    0.6518    0.6505    0.6492    0.6477    0.6462    0.6447    0.6431    0.6414    0.6396    0.6378    0.6360
    0.6639    0.6639    0.6638    0.6636    0.6634    0.6631    0.6627    0.6622    0.6617    0.6612    0.6605    0.6598    0.6590    0.6582    0.6573    0.6563    0.6553    0.6542    0.6530    0.6517    0.6504    0.6491    0.6477    0.6462    0.6446    0.6430    0.6413    0.6396    0.6378    0.6359
<mw-icon class=""></mw-icon>
<mw-icon class=""></mw-icon>
surf(M3-M2)





