I am having a hard time seeing how over-tightening the adjustment knobs would cause the saw to cut the aluminum guide rail unless it was so tight it was causing you to pull the saw up off of the guide bar to move it. The saw has solid stops against the guide bar on the blade side of the base. No matter how much you tightened them it can only move the blade in to the positive stops. If you just snug them up slowly you can get to where the saw will still move easily but not be loose on the rail. Get the adjusters to where the are still allowing a slight clicking sound when attempting to push the base side to side. Turn the adjuster very slightly clockwise and try moving the base again. Keep repeating this until the clicking goes away and the saw still slides freely. Do one adjuster at a time leaving the other loose. Once you have both adjusted check the saw to see if it is still moving easily on the guide rail. If it is a little tight go back and do the first one again. That will usually clear it up.
If your blade is not adjusted far enough from the rail (leaving ~3/32-1/8" of the rubber strip) then you would need to adjust the saw's alignment. This is not so easy on the Makita as it is all done by loosening the four screws holding the black plastic bevel adjustment pieces. The screws run through larger holes in the base permitting you to move the saw blade alignment. Beware once you do this it will take some effort to get things back into alignment. The blade should have a slight toe-in with respect to the rail, approx .005". This is best adjusted by only loosening three of the screws leaving one as a pivot point. Usually it would be the front screw closest to the blade but may need to be the rear depending on if your screws have bottomed out against the side of the hole you need to move in.
I found my cordless' blade to be closer to the track than I preferred (~1/16") and slightly out of alignment, leaving cut marks from the back of the blade, and had to go through this effort. It can take a lot of test cuts to get things to where they should be. If you decide to try I have some info that may help. Also, I have found the stock blade while it provides a nice smooth cut is very flexible and can wander in hardwood or thicker cuts. This for me has for me shown up in cuts that are not quite square to the surface. Overall it is a great saw but the stock blade has some limitations.
BTW - You can peel off the rubber splinter guards and move them over a few times before you have to replace them. I have found a heat gun works to re-activate the adhesive. Just make sure you keep it clean.
George