Well, if you just bondoed it in, would the bondo crack? Seems to me like there would definitely be some filler used to smooth it all out. I figure there will be movement between the filler plug & the original roof & twolip panel.
The original plug was put in really shabby since Ma Mopar figured the vinyl top would keep the plug and filler padding dry. I am not sure if bondo would be a good choice under the top because it would be a pain to fix it later if it ever needed it.
If you wanted a small window without a vinyl cover you could try it but I would think the metal/plastic plug and bondo would crack do to the uneven expansion when in the summer heat or winter cold.
It would be interesting to see a small window without the vinyl top. I think it would be subtle and not the first thing noticed but unique too.
