Why can a rifle that shoots say 30-06, only be loaded up to 50000 CUP, but the same rifle can be rechambered for 300WIN and loaded to 53000 CUP and still be safe?

The 30-06 loads are a bit on the conservative side, because there are so many older actions around. If your receiver is new, it can withstand the same pressures as are listed for the .270.

Hudson,
Denton is absolutely correct. Ammunition pressures are controlled by SAAMI specs. SAAMI, or the Sporting Arms and Ammunition Manufacturers Institute, is the governing body for those types of manufacturers.
As Denton pointed out, because of the many different actions out there chambered for the good old .30-06, and some of them aren't as strong as a bolt gun, the SAAMI pressure limit is actually about 48,000 CUP.
One interesting item. There have been recent reports of 1895 Winchester originals and Browning replicas being damaged by the new Light Magnum loads in .30-06.
In a strong actioned bolt gun, one can load .30-06s up to .300 Win Mag or .270 Pressures.
Good question....
Great Shooting
The Bearman

I have a Winchester M70 Classic in 30-06. I beleive this action is the same action used for 300 Win Mag and probably others as well. So as you've said, it makes sense that the 30-06 cartridge could be safely loaded close to 300 Mag pressures.

Thanks for your help.