I am scrubbing all the speculation about how they could have
synchronized departures etc. and wondering if the targets were really
junctions.

The Circle Line trains look like they blew up right near junctions
(Aldgate Junction and Praed Street Junction). Given the unexpected
delay on the Piccadilly Line, it now seems reasonable that the perp
caught the first train available even though he had ample time to get
to the platform.

Had things been running smoothly, I'm guessing he was intending to
detonate around Piccadilly Circus (a junction and an internationally
renowned location) or Green Park (another junction). Which one was the
target depends on which train you caught (the 8:41 or the 8:43)
assuming you want a synchronized blast with trains that are near
Aldgate Junction and Praed Street Junction.