I don't think it is intended based off how it works in gameplay. The condition for whether an unlanded character gets Clan or Feudalism on being given a title is whether they are Muslim. Any unlanded character that then inherits that title, regardless of religion, inherits that government type while landed characters keep their existing government type.
So if a feudal ruler has a Muslim heir, the heir will get feudal on inheritance if they are unlanded or be Clan if you give them land first then retain Clan on inheritance.
I'm also pretty sure it is intended, since it's not really the sort of thing that could happen by accident coding wise.
Someone had to put in that government type is inherited along with titles as a separate little function from how government is normally decided when a character get's a government some other way (being granted the title, being pushed as a claimant, being a peasant leader that wins a rebellion and so on).
The situation you describe on the other hand would just be the natural result of coding in two different ways how governments are determined for inheriting titles and getting them in some other way.
I suspect that the design was to keep continuity of whatever government you where already playing as, and had presumably organized your realm under.
If they could change your vassals might otherwise wipe clean any contracts you had negotiated with them by switching government types (since the two have access to different vassal contracts).
The player might also be annoyed if they lost their government type from inheriting a title (say by winning an election for instance).
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Now onto the main topic of the thread:
The Iberian Struggle is meant to give a somewhat different regional gameplay where one doesn't just conquer all the lands the same way one would do elsewhere on the map. Instead they want us to plan ahead and consider the various requirements for achieving the endings we want (and the challenges and opportunities presented by the current phase).
However in order to actually make that availible they had to ensure that just falling back on our default strategies and just conquering the place wouldn't be easier and more convenient than actually engaging with the struggle mechanics.
Essentially, even when going for dominance you probably want to end the struggle before conquering everything in Iberia (you want to conquer a lot yes, but not everything) and to time this with being in the right phase, rather than conquer first and then look towards ending the struggle afterwards.
This does lead to some problems when a player isn't actually all that interested in doing struggle stuff but still want to play in the area, since they just experience the struggle as an obstacle for doing what they want.
For a practical bit of advice, if you just want the struggle to end but don't care about getting any of the 3 "official" endings you could move your capital outside of the region and take the "Secure Iberian Foothold" decision