I don't think there was any conventional wisdom and on how limb regeneration occurs without increasing protein synthesis. Personally, I think the person who said that (Barna) is wrong/misinformed (even for a harvard professor!). They specifically meant protein synthesis is lower during stress response (of which limb regeneration is just one highly specialized variant), but we already know that's not true- in fact, whole extra stress-related proteins start being expressed which carry out special repair pathways. But maybe... if you count the overall protein synthesis amount, it seems like the cell would also shut down some non-essential functionality temporarily.

As for focusing on mRNA- biologists study where the light is, not where it isn't, and mRNA is incredibly easy to study compared to protein synthesis. It's much easier to just convert that mRNA back to DNA and sequence it and get loads of identity and abundance information.