It seems that beacons lose efficiency on a single factory if more affects it - 1 beacon is x100%, 4 beacons is x50% etc, this is not applied in calculations.

For example when choosing for beacons affecting a factory it still uses 4 * 0.5 (beacon) * effect instead of 4 * 0.5 (beacon) * 0.5 (beacuse 4 beacons) * effect

Reference: https://www.factorio.com/blog/post/fff-409

[Edit: i dont know how to move this to Bugs category, sorry :(]

[Edit 2: I think it actually calculates correctly from my observations but if you mouse over factory in helmod it displays incorrect speed]

In Factorio 2.0, the beacon effects is not linear and fixed in helmod v2.0.2.
are you have the last version?

I think this is not about calculations - those seem correct. What displays incorretly is speed of the factory - if you hover in helmod ui you will see the speed as adjusted previously, not the correct value.

That threw me off because i thought helmod was making wrong calculations.

I'll try to post a screenshot later.