You have to pay the handling fee yes but you don't have to take possession of the shipment by paying for it before having it sent for appeal - though the post office tried to tell me I did. There's a form they should fill out at the post office and then they forward it to the CBSA.
See this thread for The Whole Scoop
So has anyone physically been through customs with both pipe tobacco and cigars before?
Right now it sounds like it would be best to grab your usual 200g and only try adding one cigar, just in case people have a difference of interpretation.
I have. I came back with 8 tins(4 claimed by me and 4 claimed by my girlfriend) of pipe tobacco and 33 cigars this past January. No issues. I find if they don't ask about it, I don't tell. They want to know what you spent XXX dollars on while you were away...I start with the boring stuff and they usually just stamp the passport.
That sounds a little different from customs being aware of what you're doing and approving of it.
The question is, how much can I move with 100% certainty that I am within my legal rights?
As it stands that still sounds like 200 grams. We just don't have practical clarification on the rest.
Usually the only question I get is "have exceeded any allowances", which is no. You can bring 200g of pipe tobacco back and 50 cigars. I have never been hassled or otherwise slowed down. I do wonder about that partial duty they mention on their website but have never had an issue. Hopefully that keeps going...