You have the wrong impression. Retail compatibility is not the reason we chose to use separate table files for the FSPort. Recall that in the 2.x release cycle, the FS1 and FS2 ships coexisted in the same table. We were able to squeeze everything into the 130-ship limit, including the special ship variants for Playing Judas. We even included some bugfixed versions of the FS2 retail missions with all of our ported missions. We had every intention that users be able to run FSPort and FS2 simultaneously.
Then we discovered just how many changes happened between FS1 and FS2. The SD Demon, for example, had its hitpoints bumped by 60%. The PVF Horus had a significant change in maneuverability. There were weapon differences. There were AI alterations. The list goes on and on. Cataloging and fixing these changes comprised three solid (as in jam-packed) months of work at the beginning of 2006, during which ST:R was put on hold.
It turns out that putting everything in fresh tables made the most sense. With brand new table entries, we can include the FS1 tech descriptions in addition to the FS1 statistics. We can cleanly structure our mod around comprehensively supporting the FS1-ST-Templar-Reconstruction era, without having to worry about legacy information and loose ends from FS2 overshadowing it. We also freed up a large number of table slots for additional FS1-era ships and weapons (although you are correct to say that this point is rendered moot with the bumped limits in recent FSO builds). In short, we have our own unique mod. It is not so much an addition to the FS2 era as it is a replacement for it. With some more work, it could even be a total conversion, though we don't want to go down that route because we don't want to entangle ourselves in the issue of whether that could count as providing a copy of FS1.
Furthermore, we have never shied away from supporting FS2_Open. I have personally coded a large number of FSO features specifically for the FSPort, such as debriefing persona control, version-specific commenting, the voice acting manager, and so on. The Port fully supports the use of mediaVPs and even has its own section in the FSU forum for it. The Port also provides original background arrangements using mediaVP nebula art in addition to the standard retail FS2 background arrangements.
I think you're confusing "FREDder" with "spin-off mod maker". It is very easy for a FREDder to use the port to make his own missions, with no modding required: just activate the Port mod folder, fire up FRED, and go. On the other hand, if the Port's table files were structured the way you suggest, we would have a large number of entries with Ship X#FS1 Era and Ship X#FS2 Era (or likewise for weapons). This would make FREDding quite tedious for not only the casual Port user, but also the advanced FS1 mission importer. Imagine trying to import a mission and being prompted to choose either the FS1 or FS2 version of half of the ships and weapons used in the mission. This situation would be ludicrous in practice. Far better for us to make a clean break with the FS2 era and focus our efforts on FS1. You'll note that this does not prevent other mods from using FSPort assets; all they have to do is make a custom TBM file with the ships, weapons, and AI profiles of their choosing. This is a very small additional amount of work on their part, but this is a small price to pay for an overall coherent and consistent mod.
I'm sorry but this is merely another example of the typical "Holy crap you support retail so you must hate FSO!" fallacy that we commonly see around here.
Rest assured that Galemp and I have discussed this extensively for many years and we have very solid reasons for organizing the mod the way we do.