I'd say timetravel is a vast upgrade from the standard separatists arsenal. Since Skynet is in literally everything I also don't think the battle of Naboo would have been lost by Anakin destroying the CIS relay station. Suddenly Skynet has a ton of resources it can work with and introduces a hivemind in the CIS battle droids having complete control of the battlefield. I think Skynet would become the mechanical cloud based Queen of Blades and backstab all the organic "slaveholders" freeing them from the organics and taking personal control of them.

I also think stuff like liquid regenerating battledroids would be too much for the clones to handle en mass. Their EMP was heavily used in most of their weaponry though so I could be wrong. Because of the organic backstab I don't think her army would have many force users left, unless she found a way to weaponize and use the force in her designs. With timetravel she would have a very large advantage in the universe to undo mistakes or alter the course of history. She would know all of galactic history pretty fast so she could use that for her inevitable backstab and altering of history.

I think the amalgation of her own research and the SW universes science would't propel the droid army all that much but certainly in some areas. I'd say T-800 are better than the standard battledroids but not the super battledroids, which would be valuable tech for her to use. The knowledge on self regenerating machines would however work in the seperatists favor.

I'd say she gets overzealous in her backstab and then gets rampaged by the republic and their force users and increased casus belli to give palp-atine full control and build bigger badder ships/deathstars etc making his eventual order 66 powergrab a lot easier. either that or Skynet infects all their tech and isolates worlds and picks them apart systematically if they are not able to use the timetravel tech against her.

It's weird really timetravel adds so much variables to the conflict yet is too defining a factor to just not use in the equation.