How much would a trashed 5R transaxle be worth?
 

Code is 5R30105. Has external oil cooler and LSD according to Clarks garage. The internals are trashed. Shifts through gears, but the input shaft catches on something, and makes a clinking sound. Drained the fluid and metal chunks came out.

My question is would it be better to tear it open and part it out, assuming the parts are good, or would it be worth more to sell it as a whole?

No way of knowing whether there is anything of value inside until you tear it down, clean, and inspect.

What is the point of no return when disassembling these transmissions for inspection? Can I take the 5th gear and diff cover off and put them back without any consequences?

No you will not create any issue removing the cover or end housing from the trans.