If you don't need padding there, why put padding there?
If you put a big padded chamois into a short to protect the 'taint, yet then cut out the chunk under the 'taint because it's too thick... what's the point of the chamois in the first place?
Remember, a chamois was originally simply that: a piece of chamois leather sewn over the area of the knitted shorts where all the seams met. It was there to protect your skin from rough seams, not to protect your tush from a poorly fitted saddle.
If someone tells me they are having trouble with padded shorts, I strongly suggest they stop wearing padded shorts. They look at me like I'm a nut! But seriously, why wear padded shorts if they are uncomfortable? It is possible to go without the padding. The world won't stop turning if you buck the current fashion trend.
I find I'm happiest in unpadded UnderArmour compression shorts on an unpadded saddle. Medium length (50 miles or so) rides are so much more comfortable this way. I haven't ridden a long ride since I gave up on the padded shorts, so I can't give any data on that.
Sometimes, simpler is better.
"If Americans want to live the American Dream, they should go to Denmark." - Richard Wilkinson