I think its just tight. The extractor is a strong spring, eesistance when closig hte bolt isnt anything to be alarmed about, though it sound slike its only giving resistance when it has a round in it. The extractor may be a slight bit long in the rim groove of the cartridge. My 98 actions dont move the extractor noticably when loaded compared to not, but if yours works, it probably wont cause a problem. It could be fitted a little, but I'd likely leave it alone.
....You will have a problem trying to load a round in a controlled feed system unless you first push the round down into the magazine well
There shouldnt be any problem dropping a round in the chamber in a Mauser action, unless its a military action that hasnt been modified. The "controlled feed" doesnt by nature preclude the extractor being able to snap over a cartridge rim, the military guns just weren't done that way. There's no real reason they shouldn't work when properly set up. The front edge of the extractor can be beveled to allow this, all the commercial sporter Mausers I've seen are done this way as are virtually all the commercial actions based on Mausers, and the 1903 Springfield, and it was common for sporter conversions of miltary actions.