If you can't purchase it in the store itself, the item sells for 0g, but you CAN sell the items if you choose to.
The stopwatch is kind of a special case. You mentioned the two forms of stopwatch. You probably are referring to the regular and broken form. However, there's actually a third. The initial item you get is an unusable stopwatch that has a charge time of, I believe 6 minutes. I've unofficially named it the "Winding Stopwatch" but it DOES have a unique name. I just forgot it. After that, it becomes the regular stopwatch.
Anyway, the "Winding" Stopwatch and Broken Stopwatch sell for 0g, but the "normal" Stopwatch sells for 420g like a normal item. However, just taking Perfect Timing seems to increase Zhonya's (And possibly GA's & Stoneplate's) cost by 300g. Zhonya's for me went from 2900 to 3200, even though without taking Perfect Timing, the cost was at its normal 2900g. WITH the regular Stopwatch gained from Perfect Timing, the cost is decreased to 2600. Having the Broken Stopwatch permanently increases the regular cost by that same 300g. So I highly discourage selling the regular stopwatch unless you're planning on just using it for an extra 420g.
Actually, now that I think about it, that may be worthwhile. I never actually tried it, but that's just about an extra amplifying tome or ruby crystal on your first back. That isn't bad at all, but the PBE with runes reforged is closed, so we'll have to see if that's stayed by the time it rolls around next patch.
TLDR: You can sell pretty much anything gained from runes/masteries, but only the regular Stopwatch seems to sell for any gold. 420 gold to be specific. Everything else is 0g.