Hello,
Yes flat top batteries will fit in the battery holder, at least the ones I've tried in the past do.
By far, the best battery we've found is the EBL "White top" 18650. It seems to have longer life than anything else we've ever tried and it has some protection, but not overly aggressive protection.
The battery you chose should work, however it is unprotected which means you need to be extra careful about charging it and making sure it doesn't over-discharge. Always remove batteries when you're done using the robot, because if you leave the batteries in and somehow the power switch gets hit, you could destroy the batteries or even physically damage them and the robot due to overdischarge.
(Even EBL batteries should be removed, by the way, as a general safety precaution. You never know when the protection circuit might fail.)