Nope.
Layer combinations are only relevant to views, and views don't exist in modules. The reason you're losing layers out of the .MOD file is because .MODs only save information required for what is modeled or drawn, nothing extraneous. PLNs and the MODs derived from them are not linked though.
It sounds to me like you want to just use very ligntweight PLN files (strip out all unnecessary views/layouts/worksheets etc.) and use the PLNs as hotlinks instead of MOD files.
Scott Graham, AIA LEED BD+C
Principal | BIM Manager
Muhlenberg Greene Architects, Ltd.
Wyomissing, PA 19610
V6.5-26.0