RAID arrays with big disks is just fine, yes there can be delays in rebuilds but that's fine so long as you use something like R6/60 where there's still parity during rebuilds.
My biggest worry with this would be the 'all eggs in one basket' thing with just the one server - have you considered using a distributed filesystem like Ceph at all? You'd end up with more, but smaller, servers and could spread them out over racks for extra resilience - just an idea anyway.
What I'd think about for your main question would be to get a normal 2U server and use one or two external SAS disk enclosures connected to one or two PCIe SAS RAID controllers - this way you can upgrade your server - or storage - without impacting the other. It shouldn't cost too much either and there are lots of options, one big enclosure with all your disks or two, perhaps smaller, ones and then split the 0 bit of your R60 across enclosures - you can even 'dual-link' then to the RAID arrays for added resilience.
Oh and the hot-spares is a good idea too, definitely do that.
One final thing to consider - take a really close look at the actual disks you want to use - make sure they have a '100% duty cycle' (i.e. can be running 24hrs for years at a time), not all are, and make sure you don't use 'shingled' disks - they're fine for home use but their write speed is just awful in a server environment.
