It wasn't a .5 style upgrade at all.
First off, it replaced nothing. You were expected to use both the Core PHB and the Essentials books side by side. Nothing was being deprecated. But, again, 4e was a different animal from 3e in that the rules were constantly being updated. The dreaded Errata of 4e. But, the idea that the 4e rules were ever set in stone just never existed. They were constantly being changed. The biggest issue was that it was virtually impossible to keep up with the changes since they were banging out new rule books virtually every month.
Yes and no. After all, all the spell updates in Tashsa's are meant to supersede the original PHB. The race rules are meant to supersede the PHB and are the default in all 5e material going forward. The rules in Xanathar's, as well, add on and are considered default, not really optional. For example the rules for tool use or the newer downtime rules. So on and so forth.
Where did this idea come from that 5e was like 3e in that you had core and then nothing else? 5e's been pretty explicit that anything and everything adds together. If you filter spells for "Core D&D" on D&D Beyond, Absorb Elements shows up right there at the top of the list, right above Abi-Dalzim's Horrid WIlting, despite both spells coming from the Elemental Evil Player's Companion.