We currently do both. Random generation is only done if there aren't enough prescripted ones. The ones the OP are complaining about are manually preset estates. These roughly reflect history and means that some countries will have to handle their estates a bit if they want to have optimal use of their land. This is intentional, the estates are factions that existed before you took over just as much of the setup in 1444 varies from tag to tag. Obviously estate land ownership is something quite abstract so you can probably find some things in the initial setup to disagree with but the idea is that it should reflect history rather than what is optimal. If you do find one area or another to not have a setup you agree with going from history then I suggest bug reporting with sources and it may be changed.
However an early modern monarch having to trample the rights of the nobility, burghers or even clergy to make the most of his country seems far from odd to me and reflecting this is in fact one of the major goals of this system
It's not that hard to confiscate and reissue the land as Castille, I did it myself in the dev MP recently.Some tags also start with some estates more powerful than others. Mamluks will have stronger Amirs entrenched in more land. The Indian Sultanates will have more powerful Dhimmi factions, and so on.
EDIT: The England issue reported in this thread on the other hand is a bug and has been reported as such in the bug forum
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