With most actors, they'll negotiate a fee based on work (episodes).
It's usual to stagger payments. So if his fee for a Dr Who season is 200k, standard is he'll probably get 80k up front, 80k half way. Then the remainder post prod completion.
Royalties for repeats have changed, he may have accepted a one-off payment and waived UK rights, else probably gets several thousand per repeat upto three repeats, then gets nothing.
As for his royalties from merchandise, I can assure you it's tiny tiny tiny ! Pat Stewarts merch income from dolls, imagery etc is IRO 20k pa he says, and that's a worldwide brand !