Yes, my thoughts are that we don't really understand Ishamael's limitations and "status" - we're purely guessing. The Head of the BA was found dead in a ter'angreal, it doesn't prove that Ishamael could enter the real world back then. If he killed her in TAR and had ordered her into that ter'angreal, she died in the real world too... We know Ishamael rose Alviarin in her place, but again we don't know if this was done in the real world. Alviarin herself may not fully know this. We also don't really know if once he's able to enter the real world, this is a "permanent" thing, or one that require special efforts, or one that for many years is "on and off", before at some point Ishamael is really free.

It's perfectly possible, in fact likely, Ishamael was restricted to manifestations in TAR or in the area SG (where his fortress is) until the end of EOTW. His apparitions at SL, but the fact he didn't appear before nor took a further direct hand, seems to indicate he was struggling to be able to enter the real world at that point, wanted to but wasn't able to make himself "real enough" to leave TAR, merely able to open gateways to the real world from it, but not able to step through and "be real", it seems. As for his status 20 years ago, we have much too little to be certain of anything.