Welllll... my first thought was "They hurt because you have not gone out shopping at a saddle shop with every brand under the sun and not stopped until you sat in the right one!"
I'm in your boat, too. I don't ride western myself (unless someone threatens teeth pulling :p)... and, as such, have never had a need to go saddle shopping for one. I suspect my bruised seat bones from every Western saddle I've sat in is because they weren't bought to fit my body!
Western style seats of the correct size for the rider are among the most comfortable (otherwise we could never have spent so much time in the saddle working cattle). To small and they're a pain. When they're larger than needed it hasn't bothered me, but after 3+ hours in one that's too small you're lucky if you only have one area that hurts. If you do a lot of riding you'll want a large enough and a relative flat seat so you can adjust your postion to what's most comfortable. If you're ride is long enough you'll likely find that you'll change your position in the saddle at times. That's one of the reason a smaller seat creates aches and pains. You can't adjust your position for your comfort.
The real problem with Western style saddles is they have a horn (something not needed unless you're roping) and they weigh a ton (something the horse really doesn't need), but if well fitted they displace weight pretty well.
With the exception of the child saddle my granddaughters use (with no horn) I haven't owned a western style saddle in almost 20 years.
If a full quater horse bar fits your horse you're lucky. Be glad you don't have one that's to big for that and to small for a draft saddle. It's tough to even find someone who will custom make a saddle for a horse that one of the standard sized trees won't fit. Thank goodness for Universal Pattern and Troopers.
If you do a lot of riding you'll want a large enough and a relative flat seat so you can adjust your postion to what's most comfortable.
Well, this depends on your preference and your body. The reason that Roper trees are so uncomfortable for me is the flat seat. If you look at almost every ranch saddle made, they have a relatively narrow twist unless you request it wider, and they have a deep seat pocket that sort of cups your seat with the part of the seat closest to the pommel being built up a bit (how much it's built up also is a personal preference).
Like this. Looks like it should be really comfortable, right?
Nope. 3 hours and I am aching everywhere from my stomach down.
However, I can ride in this for 10+ hours and get off feeling just as refreshed as I felt when I got on that morning. This is an old picture, but it really shows the seat pocket better than any of my newer pictures.
Get your feet / legs under you more. Try riding with the stirrup a little longer.
You could be sitting to far back on the saddle. The saddle /seat could be to narrow. I have a roping saddle I like and an A fork saddle .