If I boot my Win7PE SE ISO it automatically assigns drive letters to all partitions even if they are not NTFS,FAT32,FAT etc (they are non windows file systems)
My Gena build (XP) does not do this!
Behaviour difference is an Interesting info.

What is the format of these partitions on your case ?
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I don't know a setting "don't mount unknown format partitions"
There is one:
Finals\Optimization plugin
->"Don't mount local harddrives"
That I guess will not mount any drive letter.
This is a setting for special cases where you want to inspect disk and be sure nothing written during pe boot.
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btw, since you are transfering to new PE, maybe better use Win10PESE, it is very mature by now,
also Gena 2k3 maybe still useful.

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Let us know if you have progress.

