My D-Tek heater core is mounted just like you said... top of the case horizontally, with a blowhole directly above it... I squeezed it into my top two 5.25 bays. Haven't had a single problem.
The only thing I don't like is that if I want to use one of those bays, I'm outta luck. It's the only place I can fit it though in my case, even though I have a Lian-Li pc-60 which is fairly roomy. Will NOT fit down in the lower front of the case.
Btw I suppose depending on your config, it could be a 'bear' to bleed your system. As long as it's securely mounted though it won't be a problem. Mine isn't bolted, but it sits completely tight between the walls of the case. So I just shake the case from side to side when I need to bleed it.