I switch to pancake mode whenever I do extensive SRV stuff, and I've never had a problem. I need 3rd party software for one of my joysticks, and if I log in and can't navigate menus, I immediately know I forgot to load that software. But if I load everything correctly before I start, it doesn't matter which mode I'm in.
One thing that I haven't been able to figure out, though, is no matter what mode I'm in, my DSS axes always revert to a joystick axis and I have to unmap it to use my mouse. Every time. I don't know why, but it's the only binding hiccup I have to deal with anymore, so I don't complain.