As you note, the three ¼-20 fasteners are surely not up to the task of altering the shape of the heavy gauge aluminum cover to force it to seal. Below are some solutions to consider.
Start by trying a Cometic foam gasket (aluminum frame with nitrile rubber foam on each side) which is 0.060” total thickness. Hopefully this will solve your problem.
https://www.ebay.com/itm/Harley-58-69-P ... Swke9aTXNBIf the seam still leaks, I’d advise being more aggressive and sealing it together. My go-to procedure for this is the following. Clean both sides of seam with solvent and get it absolutely squeaky clean, i.e., free of any oil, debris, old gasket residue, old sealant, etc. Then carefully and quickly apply a uniform small bead (1/16” dia) of Permatex Ultra Grey silicone sealant to the cover (do full circumference of all holes), assemble immediately onto dowel pins and secure with the 3 fasteners. Wipe away any excess silicone that squeezes out of the seam with a small amount of mineral spirits on paper towels or Q-tip swabs. Allow 1 day to cure. If you’ve done this properly it will be dry for the rest of your life.
Many people dislike silicone sealants, and if that might be the case here, there are myriad other sealants to explore – Wellseal/Yamabond/Hondabond/Threebond, Loctite 515 & 518, etc, all of which may also work to seal the subject joint if you are averse to silicone.