We're customizing weapons not cutting a baby in half. What's the worst possible thing that could come of increasing fire rate or magazine size?
Well, if you want to inject reality into it, the larger the mag, the more potential for feeding jams. Increased rates of fire increase jamming rate, mechanical failure rate, inaccuracy, and potential irreparable damage, like warping barrels.
Like any mechanical device, design decisions and mods almost always have performance tradeoffs. To not have them in game is understandable, but it's not realistic...another design tradeoff.