"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
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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
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surf(M3-M2)