I'm sure you can do what you need with their ^ recommendations but I do it differently and though I might offer a different idea.
I was going to build with pvc/poly as well until one day I was sitting in my office and I started thinking about using map tubes like these:
Telescoping Drawing Tubes
#1 I wanted one big enough to hold multiple rods so I wanted a 3" diam. 3" pvc is starts to get a little heavy/ unweildy at that point.
#2 I wanted to make sure I could easily travel on a plane with them. Some airlines have different dimension requirements...so something adjustable- like a telescoping tube- would allow me to change size based on rod size and carry-on limits.
The only modification I did was to glue a couple tiny plastic stops along the sides to keep it from collapsing past a certain point so it won't crush the rod tips.
Cons: It's not completely rigid, but it still protects well enough so that it won't damage anything (I wouldn't drive a truck over it)....and I strap it down hard
against my gear pile. It also won't hold rods with reels on them.
Pros: Lightweight, adjustable, can fit up to 5 rods in it, comes with a shoulder strap...and it cost me $5 and didn't have to do any work
Some thoughts as to why I didn't cut slots in the side for the reels:
-I decided it was more important to keep the elements out. I didn't want water (or dirt, leaves) getting in there and staying there.
-With the reels left on it's an awkward shape that is hard to pack.
-It takes away from the protection (could technically rip a reel off it's bed)
-If you are fishing, it will be out and rigged right? so unless you are doing like an 8ft+ tube, you'll still have to assemble the rod anyways.
-Cutting a slot limits you to one rod and reel
-and maybe most importantly, because I've done it before
for fishing rod holders on my boat and inevitably some rods and reels just won't fit that well. I don't know about you but sometimes I spin fish, mostly I fly fish and sometimes someone has a baitcaster and my GF uses a spin caster. All of these have different reel seats and dimensions and no single cut will cover them all....You may say "well I only spin fish" (or something). And I can tell you that all of my spinning combos would require different slots (diff; handles len/shape, spool clearance, neck width, spool shape etc.). Same with the fly rods. If you buy a new rod or reel, it won't fit the same, seriously it's just easier to not have a slot.
I say make it fully enclosed and all about the safe transport....just put the reel on when you are about to fish.