I will not argue with your point since, frankly, I do not care who is at fault. MS have a license for Here Maps and bought Nokia, which integrated 'Here' into the Lumia phones, which Microsoft bought. If I buy (or own) a Lumia, I now have a Microsoft phone. If that phone is deficient, then I hold MS responsible. My 'Here' web-based interface syncs with the 'Here Maps App' on my phone. Microsoft can readily have my full permission for its map app to do the same. However, if MS built its app to be incompatible with the preexisting Here app, that is MS's fault. I had no other maps on my phone, prior to the WP8.1 update, only 'Here'; so MS have introduced the later app, and should have ensured it was compatible. If the MS app was first, and already incompatible, then it should not have introduced it as the mandatory basis for Cortana, at all.
You can come back with all the technicalities you like, but as an end-user, I do not care about the problems of MS or Nokia; I only care about my problems. My problem is that I can spend countless hours, ploughing through my hundreds of place-marks, manually entering them into a new, inferior mapping application, which I will rarely use except when Cortana does so; or have them unavailable to Cortana (as far as I understand it, currently). Worse still, we know full well that this will probably all change, in some way, soon, and all that work will either have been unnecessary (because MS makes 'Here Maps' available as a default) or, even worse, MS introduce some entirely different app that requires I do it all over again. No thanks - I would rather just ask Cortana to open Here Drive and select my existing favourite places manually. It just seems a shame that I will have to do so, that is my point.
Obviously, the alternative to all this is that 'Here' will hope to avoid some users choosing to enter future Favourites into the native app, by making its products more integrated, from its end. However, if people choose to go this route, if they 'save current location' as a favourite whilst in 'Here Drive', then they will have to do it again in the native app. To me, this seems like a complete mess, which it most certainly was not, prior to the introduction of the MS maps app.
I should add the proviso, as previously mentioned, that I am making these comments without actually having Cortana, yet; so I will certainly reserve full judgment until I know what is the reality.