You can't use Sigma gear for Valence Fusion, since it doesn't have any randomized stats. Only the house stuff you find in mission works like that.
The Sigma stuff is overall cheaper and easier, but I'd consider it "starter" gear. Once you get a decent MKIII house part, break down the Sigma equivalent into resources and stick with the house one. Not only are the stats better, but it also comes with a unique passive, like a chance to put fires out automatically.
With the latest changes to Railjack, you could probably get by with all Sigma gear for a while, but I'm anticipating that the devs have loads of Railjack content coming up that will ramp up the difficulty.
So to answer your question, no, don't buy a second Sigma MKIII reactor, there's no point.
Ikusi_Prime's post in Valence Fusion for Railjack was marked as the answer