I've been thinking that Kayaba won't be able to directly interact with UBW.
But, like... That's more because it's fundamentally an "analog" virtual world, rather than a computer/digital one. So rather than it being
impossible for him to hack into it, first he has to write, like, an entire
interpreter and he just straight-up doesn't have the time.
I'm not decided on how much he knows about UBW yet; certainly he knows that Shirou has some kinda crazy something going on, based on his reports. Honestly I want him to figure out that it's a Marble specifically (instead of something whacky inherited from Kerry or whatever) later, during the Origin Patch, so I can tie the whole Reality Marble thing together with "approaching your Origin" when he's in a position to be expositing on it.
And messing with Shirou is very much "fixing something that isn't broken" for him right now.
I've been debating that Kayaba railroading Shirou into being the Final Boss is, just a convenient and useful cover to his real objective: isolating Shirou in a Workshop where he can manipulate Shirou into really min/maxing his character sheet once an OP prestige class gets unlocked, so to speak; that way Kayaba can research a Marble
and increase the fighting power of someone that explicitly prioritizes human lives above the Statute of Secrecy.