#8 THHN in Conduit for 50 amp circuits
YES. 

I can't vouch for what "3-wire set" means.  I suspect it only made sense in context of that other question (you didn't get it out of NEC). 

Cable in Conduit: Yes actually, but it sux

You ARE allowed to run cable in conduit, in two modes. You can either use it as physical armor only (for which sched 40 PVC is inadequate), or you can use it in the conduit wiring method, however that requires excessively large conduit to meet the fill rules.  Both require excessively large masochism to pull those stiff, balky things.  Not a job I would want!

The three grounds/1 ground point problem can be solved by pigtailing.  

A single circuit of 50A is allowed to use #8 THHN, if the terminations at both ends are rated for 75C temperature.  You cannot use #8 NM or UF cable at 50A, because it is not allowed to go to 75C temperature. (but weirdly, NM-B uses the 90C column only for the derate I'm about to describe.) 

Thermal derate

Let's go through the math.  NEC 310.15(B)(3)(a) requires you derate conductors based on how many are in the pipe. In split-phase systems, neutral and ground don't count, so you have 3 circuits and thus 6 wires.  6 wires requires a 20% thermal derate off wire max. 

The only thing in the conduit is THHN wire which is allowed to 90C (terminations aren't, but they're not in the conduit). As such, you can use 55A as your basis.  The 90C number for #8 is 55A.  

That derates to 44A. You get to round up to the next breaker size. Nobody makes a 45A breaker, so welcome to 50A.  

Conduit size and aluminum

You'll need 1" conduit for seven #8 Cu wires.  If you use 3/4" EMT metal conduit, metal conduit is the ground, and  six #8Cu wires will just fit at limits. 
Aluminum might be your friend

You could use #6 aluminum instead for cost.  There's nothing wrong with it at these large sizes. However if the water heater's terminations are not rated for it (CO-ALR) you would need to pigtail the aluminum wires to #8 copper. Price the needed Polaris connectors versus the savings in wire. 

You need 1" conduit for six #6Al wires + 1 bare Cu ground.