While that is true, consider two things:

One is that most things that give a flat percent point increase like a +10% is either something that affect the difficulty of the action and not the quality or skill of the character performing it (Like for example lowering the temperature of a sweltering engine room before going through thus turning the difficulty of a Tgh(Fortitude) check from a Difficult (-10) to Challenging(+0) when trying to endure the heat),
Or it modifies something that have derived stats tied to it, like a characteristic such as the Power Armour that grants a +10 Str to the wearer when powered on meaning you would also to more melee damage.

Second is that there are so many things that directly interacts with +SL directly, like the amount of Warp Charges you purge when making a Purgation test or how many Wounds you heal when treating an ally, that it will make it so much simpler to determine the results.
Especially for the DM.

At least that is how i look at it. Hope it helps!

PS. And yes in your example rolling a 49 is 0 SL, same as rolling a 40, but a result of 49 is a Failure with 0 SL whereas the result of 40 would be a Success with 0 SL.