I'm confused why some Reaper (config, ini, and such) files are stored in appdata/roaming/reaper and other Reaper files are stored in the program files/reaper path? Thank you.

Interesting thought. Have you also looked at where the Windows related files are kept on your computer? (assuming you are not on a Mac)

I think that Makes Sense 

Seems like Fabian's guess is correct (storing different application data for different user accounts) :) In general, it probably also varies or depends on the application and/or software company where files are getting installed to under Windows. Some are putting certain application data files into location A, others into location B, and so on ... Basically a similar 'issue' as with certain plugin installers (which have fixed install locations) from different companies, so you are ending up with having multiple plugin folders in different locations :D

AFAIK, in the old days, reaper used to install on windows much like it does now for a portable install... then with Windows 7 things changed and I believe it was M$ that required reaper and other apps to do their installs in the Micro Sauce manner.... I much prefer reapers portable install but do keep a normal install on C drive as well... but the one I use daily is the portable on D drive.... the portable does not give rearoute, nor rewire but I don't need those often... if at all...

Users can't nor should write to program files, it's a protected folder, so writeable copies of settings files etc go to AppData. That simple and for good reason as far as security goes. In some cases where apps don't follow "security protocol" Windows will silently write to the AppData folder, again for security reasons. If you want deeper details...