Technically it shouldn't be, MC is the character whose POV we get most of and ML should be the love interest. I remember when people first started using MC/ML for bl they did so because they were tired of ppl referring to them based on their sex positions (seme/uke) but now for a lot of people it's become a replacement for it. Like if you're gonna say the main character is ALWAYS the uke and the male lead is always the seme at that point just use seme/uke.
Usually in straight romance, we use ML and FL (male/female lead) for the two main characters irrespective of whose pov it is from. But in BL both are.male so using ML for both us useless. Thus the trend started to call the person who is the 1st main character to be called MC and the partner to be ML (male lead).. so no, its not the uke who is always called the MC, its the 1st main character irrespective of what position they take during the act..
Though it is true a lot of the time the MC ends up being the bottom. But there are stories where MC is the top too like this one. Mokyeon is the MC bc everything else is based around him.
There is also "Perfect Omega" where the MC is alpha and top.
I just learnt that uke are always considered MC in yaoi, from this very comment section. They said even if the story is following the seme, he's considered ML because he's seme ╥﹏╥ what a strange concept, but whatever floats your boat