Yeah,I had this issue putting fenders on my Ti Motobecane. On the left dropout the frame has this 'ridge' right where the braze-on is. Had to file a flat side on a spacer to move the strut out. The braze-ons are badly placed,but then I think they were an afterthought since I think they intended this to be more of a race machine.

Those two upper holes on the left side are for a disc caliper(mine had discs). By mounting there,the left side will be higher than the right(unless the rack legs are adjustable). Might want to look at a rack whose lower mounts go on the skewer. Def need to tighten up the mounting on the right,it needs to be up against the frame.