But sometimes mount point is different and you can get "/Textures/t.1" from additinal paks even from games built with latest UE4 versions. There is no way to somehow "respect" this, because mount points are making sense only for UE4, where all paks are handled as single structure, while quickbms and unrealpak works with each pak separately. Though I think some workaround can be implemented in base script, if you provide some particular example (I've only done it for Fable Legends script, which is obviously can't be used with latest games).
Can you elaborate, may be I never encountered it? In the pak, the first entry in name list is the root entry. For example, let's say you pack Content/Data/ and Data contains Materials/, Scripts/, Whatever/. The first root entry will be "Content/Data/", depending on where it is, can be ".../Content/Data/" or "../../../Content/Data/" but it will be there ALWAYS. if you are packing multiple entries in root entry like, Dir1/, Dir2, Dir3, then, again, depending where these are in the hierarchy, it will be either "../" or "../../../".
What are you saying (if I understand it correctly) makes no sense, there could not be 2 root entries or files OUTSIDE of it. Whole logic behind PAK structure limits it.