Another thing is you have to basically discount the Pilot episode, since that made it clear Tony was THE boss, and was retconned afterwards to be what is basically the Underboss; he seems to be higher than just a capo (although probably in the hierarchy is a capo) but that could just be because the focus of the series was on him so he had to be made to do more than he should.

I think when Junior became the boss, for all the reasons stated (placate him, make him the focus so when things crash down it's "not a young man with a family" etc.) Tony becomes what is basically the Underboss, but he still defers to Junior (see: Hesh) but does his own things to manipulate because he's the guy everyone else goes to with problems.

Junior technically remains the boss, on paper at least, until probably his dementia starts to kick in. Just that Tony handles all the day to day affairs so is the boss in name only, but never actually became the boss, he's always the Underboss/Street Boss who just takes care of everything like the boss.