The connection between HL and Portal is just a cameo, to me. In Portal, writers couldn't resist the temptation of quoting and referencing HL, but we shouldn't read too much into that. Neither should we expect a rigid and coherent timeline. Portal has to be considered a stand-alone franchise.
This.
I believe the references to Black Mesa seen throughout the course of the game (e.g. the performance charts seen in various offices) are merely devices used to enforce the image we are given of Aperture Science, which is that of arrogance and an almost desperate need to be ahead in their field (which was their undoing in the end), while at the same time giving players something familiar, and the context, rather funny to relate to.
Uhhhh, did you play Episode 2?