Should be easy to do.
Secure-hook FCF_SetChatWindowFontSize and provide a database where keys are the chatframe IDs, and the values are the font size.
Then, when UPDATE_CHAT_WINDOWS/PLAYER_LOGIN fires, run a "SetFont" on each chatframe.
EDIT: I'm an idiot, I misread OP's question
EDIT2: I know for a fact that you can copy chat-cache.txt and layout-local.txt.
EDIT3: ElvUI sets up chatframes at installation, my unreleased addon
Clackity uses a similar approach.