I know nothing about multi-layers and your answer did not understand.
Simply put: Imagine you have a piano soundfont instrument which is arranged like this:
Sample 1: C-4 to B-4
Sample 2: C-5 to B-5
Sample 3: C-6 to B-6
OpenMPT always imported this correctly with three samples.
Now imagine a more complicated piano instrument like this:
Sample 1: C-4 to B-4, playing at volume 0 to 31 (soft hit)
Sample 2: C-5 to B-5, playing at volume 0 to 31 (soft hit)
Sample 3: C-6 to B-6, playing at volume 0 to 31 (soft hit)
Sample 4: C-4 to B-4, playing at volume 32 to 64 (hard hit)
Sample 5: C-5 to B-5, playing at volume 32 to 64 (hard hit)
Sample 6: C-6 to B-6, playing at volume 32 to 64 (hard hit)
As OpenMPT can only import one sample per note it previously imported just the "hard hit" (or "soft hit", depending on which order they appear in the file) samples and ignore the "soft hit" samples. If you wanted to use them, you couldn't do it without resorting to external tools liek Viena.
Now with OpenMPT 1.29, all six samples will be imported, but the "soft hit" samples will not be associated with any instrument. You have the chance to set up your own instrument to use them without using a tool like Viena, or you can simply delete them.