I can attest to the fact that roof penetrations for chimney flues will leak. I suppose you could prevent it with annual maintenance. We just accept that leaks will happen. We have one of those rubberized chimney flashings but it's not perfect.
This is the outside before the decorative canvas went up.
Then another (we have 2 of these gers) with final, decorative canvas installed.
The leaks occur on the top lip. Either copious amounts of sealant which tends to last only 1 year of our extreme weather, or an extra fly sheet would prevent this entirely.
So, I can think of experiments I could do with a mini-fly sheet just for the segment of roof with the chimney but the chimney pipe still has to go through somewhere. It'd have to be heat resistant. I've had my fair share of burnt canvases touching single wall chimneys. That being said, our chimney is double-walled and insulated so probably wouldn't burn/melt.
We didn't really see the advantage of a side venting stove because our walls are curved in the vertical axis too. So there'd still be leak risk there too.
Traditional Mongolian gers do leak. However, it's not a rainy climate. So they get wet and then they dry in cycles of wet and sunny weather for just the short summer. They aren't waterproof. They are designed to breathe. We just accept some leakage and deal with it. Most traditional gers just have roll vinyl floors and are easy to mop. If some rain gets in.
If you're in a temperate climate, like the UK, or the USA's PNW where it rains all year round, I think a side vent might be a better approach.