The penalties are not different between species. Laws are written such that penalties are 'up to $5000 fine', etc. so that judges have some leeway with sentencing. Hopefully, you would be fined a small amount for a ball python compared to what might result from a mamba! It is up to the judge, though there are often recommendations from attorneys.
I believe that in the Toronto saw-scale escape incident, $14000 in fines were levied- $1000 for each prohibited species. This is unusually high, I think, but it reflects the severity of the situation- multiple highly dangerous specimens poorly enclosed in a multi-unit dwelling, and one escapes...
And although Lisa is correct, it is extremely unlikely that anyone is going to be given a permit for an eastern massasauga by the MNR.