YNAB does support multi account split transactions, it’s just a combination of the split and transfer types. It’s not meant to support full accounting but it certainly supports that.
YNAB is basically completely useless as far as anything beyond an extremely extremely rudimentary single user budget.
I’ve never had YNAB double up a transfer.
Also, capital gains - not sure what the issue is there either. Add a transaction and categorize it to “Ready To Assign”. Works great.