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1.) With these router bit sets, all of them cut the rail/stile to some shape, would it look weird if I profiled the panel with a bit, then just left the rail/stile square with a groove in it to accept the panel? Looks like those bit sets that Bill showed have a lot of good profiles and some that are a simpler profile to make sanding easier as was mentioned.
If you don't want a profile, you can make a frame, perhaps with mortise and tenon construction, and cut a groove for the panel. You can even do that, and use a roundover bit on the assembled frame (clamped but not glued), and fine tune the corners with a chisel. Or you could spring for the rail and stile bits like everyone does.
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2.) Never thought about the panel be flush with stiles/rails, not sure it matters to me, but if I did want it one way or the other I would just have to change the panel thickness correct?
3.) Whats the panel bits with "undercutter", I don't need that do I?
It is far easier to sand the whole door or whatever if the panel is the same height as the rail and stile. Oversimplified, if you want a 1/4 inch groove in the middle of a 3/4 inch frame, you need 1/4 inch above and below the groove. Therefore, the panel should have 1/4 inch above and below the tongue.
In practice I like the panel farther forward, so the groove is maybe 3/16 or less from the back and 5/16 or more from the front. The back cutter, with a fixed 1/4 inch spacer (or whatever to match the rail and stile groove) makes the cut very easy, but I have on occasion used
part of the profile of the front cutter to do the back. The back cutter is worth the investment.
Some factories use 5/8" panels rather than 3/4 inch so they don't have to do the back cutter. To me that looks cheap.
Since I am spending your money, two more things to watch for: Many rail and stile sets have a groove 3/8 inch deep, which means the tongue/tenon on the rail is only 3/8 inch long. Better sets have a 1/2 inch tenon and groove.
!/4 inch is a common groove width in the American rails and stiles, but 5 mm is common in Europe, so those cutters only have a groove and tenon about 80% as thick. Be sure your set is consistent - check carefully if you mix brands.
If you decide to use flat panels at some point, the 1/4 inch American plywood is enough thinner that it rattles in the 1/4 inch groove. However, when I veneer one side of 1/4 inch plywood the rattle becomes insignificant. Why? Typically 1/4 inch plywood only has one good side. I put fancy veneer on the back for the outside of the door, and the factory veneer is adequate for the inside of the door.