Basically, there were a lot of uncertainty about whether or not Disney were going to continue partnering with the BBC on Doctor Who, which in turn meant the BBC couldn't plan for further seasons – it's hard to make plans when you don't know what the budget is going to be and things like that. And Gatwa is an actor that's very much in demand, and being committed to a show that is going on a hiatus for a year or two and may or may not be renewed after that puts serious dampers on his career opportunities. So he asked to be released from his contract, which meant they had to do a whole bunch of last-minute rewrites and reshoots for the season 2 finale.
I don't know what the financials are for BBC, but I don't know that the extra money from D+ did the show any favors really. I mean yes, the production values were greater, but did those really matter? I, for one, would be perfectly cool with Tennant1 or Smith production values, with good writing and a return to seasons of reasonable length (13+ episodes plus Christmas specials). Heck, I'll take Eccleston production values.