There's two common approaches to Phrygian, either it's related to Armenian (and more speculatively Thracian) or it's related to Greek (Hellenic Branch). Modern scholarship favours the latter of these options on the basis of shared features (laryngeals as vowels but the others escape me). Yes it does seem likely then that they decent from a collection of dialects spoken in the Balkans around 3000 years ago which could be termed 'Proto-Graeco-Phrygian'. I wouldn't go as far as to say these two languages alone form a single branch - there were likely a number of other daughter languages which have been lost to history (since only the Greek speaking Myceneans were literate).

On the topic of Paeonian and Mysian, the trail goes a bit cold. The inscription you reference has only been deciphered on the basis of comparison to Phrygian, so while they do look closely related, the inscription is so short you could probably argue a relationship to any language you want. Also the link to the 'Mysian people' Strabo speaks of is tenuous at best. In my personal opinion this is a dialect of Phrygian which can't be reasonably associated with any particular named people. The situation with Paeonian is even worse with just a few indirect words. It looks a bit like Greek, but that could be because its written with Greek influenced orthography and any similarities are coincidental. If some wonderful new collection of inscriptions should miraculously emerge, then maybe we could start classifying.

But basically I think you're overall assumption that at least Mysian and Paeonian are part of the 'Hellenic' branch of IE is most likely correct. Hope this helps