Let me list a number of additional problems here:
1) Your point system will not be balanced
The first few iterations of you point system will not be balanced. Maybe the points for the T1 rules lead to everybody only ever building T1 units. Or the opposite, nobody cares because its not enough points. What do you do in that situation? You cannot change the rules without invalidating all speedruns that have been already made with the first version of the point rules. And if you do, speedrunners will leave faster than you can blink. Nobody likes to spend months perfecting a speedrun to then have the rules changed some weeks later.
2) You could have balanced the maps instead.
If you do adjust the rules over time, and by some miracle speedrunners keep up with that, you might create interesting speedruns. But if you think about it, instead of balancing the points, you could simply have balanced the coop maps instead, giving EVERY player a better variety of choices and a better experience, not just speedrunners.
3) Rule Discoverability
If i watch a speedrun of any game, and i already now the common speedrunning categories, i can simply search on Youtube for "glitchless multiplayer 100% speedrun" and i will know that o will get a speedrun if one exists, that was played exactly like that. I dont have to search in forum threads for weird rules and understand those. I already know all the most important restrictions and conditions. Creating you own rules on top forces people to find and understand this thread and maybe even check for which version of thye point system the speedrun was made.
So you are actually making the speedruns less watchable, because the viewer needs to understand much more to make sense out of the rules. This point is absolutely massive, it impacts how interested non-involved random people that dont read every post made on FAF forums are going to be in FA speedruns.
4) Game balance changes
There is a reason why the speedrunning community likes to stay on a very specific version of a game. Its because of the same invalidation problem as in 1). This isnt addressed here at all. There needs to be a balance mod that either fixes the current balance or is adjusted to some initial version of the game, so that speedruns at least arent invalidated by balance changes, because maps changes are already going to be a pain for speedrunners. This doesnt even exists yet as far as i know on FAF.
5) Community split
Whatever you do, there will be people that just use the existing speedrunning categories already used by thousands of games, often without modifications, and who will ignore your point system. There might even exist some speedruns already. So you end up with two separate rulesets, which increases the chance of the point system having less speedrunners and therefore dying.