Actually it's the Surface Transportation Board, not the FRA, that would regulate trackage rights. I'd recommend you look at the STB's website for decisions:
http://www.stb.dot.gov/decisions/readin ... e?openform
You can scroll down the list and read the various types of filings with the STB which will also include trackage rights (sometimes permanent, sometimes temporary).
With regards to a Class II/III railroad requesting rights from a Class I railroad - one thing is for certain, the operating unions for the Class I will come out in force against it. Why? Because most Class II/III railroads are non-union, and the Class I operating union sees it as encroaching on their work territory. If the Class II/III railroad happens to be union, their employees are likely paid less (and thus the Class I could use the arrangement to replace higher paid workers with lower paid workers, probably from members of other unions.) However the STB routinely rules against the Union.
Does the Class I have to give up rights? No. It's private property and the Class I doesn't have to allow anyone access to its property. But clearly trackage rights often can benefit both parties, or the Class I is willing to work with the other railroad for some other reason (financial/money, "you scratch my back, I scratch your back" - which is usually the two Class Is requesting trackage rights from each other).
Here's a good example of what you are looking for:
http://www.stb.dot.gov/home.nsf/case?op ... FD_34883_0
(this is a request for trackage rights between Salem and Portland on the UP mainline, which allows P&W to more efficiently run a former BNSF train between BNSF's yard in Vancouver, Washington to P&W's former BNSF yard in Albany, Oregon.)