Many people get coaches to the game or drive because it is far cheaper than public transport. People from Wales or the Midlands aren't suddenly going to start taking trains when they drive and split the petrol.
Goodison is not difficult to get to on public transport at all. Stanley Park alone holds 1000 cars and is very busy every match day. Those cars are not going to disappear with a stadium on the docks.
You've also ignored the space issue. Clarence dock does not have the construction potential that BM combined with Nelson does.
I'm curious though, as to why you think Clarence dock would be 'de facto city centre' when BM is less than half a mile away ? If we were to build on Nelson also it's about a seven minute walk from one site to the other.
*six, according to Google