How about having cross- or same-platform interchange shown by having both
lines go through a single circle, rather than having two joined circles?
This might make the map look a bit simpler, too. Or are you reserving that
for shared tracks only?

That's the major problem - if I will put cross-platform interchanges
in one circle, then how would I mark the stations which some line
passes through but does not stop (like Neasden for Metropolitan and
Jubilee, or Chiswick Pack for District and Piccadilly). I was thinking
about half-circles (to the side of the stopping line), but it looks
somewhat weird (especially 'cause it's only for 11 stations).