I believe some Murano pieces didn't have finished pontils, some Salviati fazzolletto, for example. I also seem to remember that some early Venini had a very specific type of pontil mark that could be be felt, but I'm less sure of that. I'll check my reference in the morning.
I wouldn't rule out a piece piece being Murano only because of the pontil not being finished, but it would lead me to doing much more research on the piece. If you have a piece that fits into this category, it would be much easier to provide guidance if a picture were provided. A specific context tends to lead to a more conclusive answer.