That IS the sealant you want to use!
I bought my replacement from one of the generic online skylight manufacturers ( can't recall the name of the place now), but, you give them the measurements you want, and they make it. Only thing you have to be carefull of while measuring, they don't have as wide of flange as the skylight installed by Monaco.
I used a thick bead of Surebond under the flange, over the new and old mounting holes, then a 4" strip of Eternabond tape over top. Unless something strikes the skylight, I don't expect any water issues!
You will have to drill new holes if you go this route. No big deal!