As you have found out, the difference between two, say TRE, headers are the contained offset values pointing to data sections in the TRE data area. In a NT or pseudo-NT GMP subfile the offset is always relative to the start of GMP header. But in a non-NT TRE/RGN/LBL subfile, the offset is relative to the start of TRE/RGN/LBL header respectively. So, for example, after you join a TRE header with its TRE data area (both from a pseudo-NT file), you need to update those offsets in TRE header to be relative to the start of the TRE header.
The location of an offset within a non-NT subfile header can be found in the document below.
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