Agreed, The new work shop is really confusing :/
Anyways, I don't know if this is how you compare items and if this is the only way, But this is what i noticed.

Say, You Had a gun called "Corn" ( Idk ) which you just got from a box.
And you had Demolisher Mark 3 on your mech, And you wanted to see which is more powerful or better for your mech.
Just drag Your new Corn from the inventory, Over to your mech, And hover it over the demolisher mark 3. And it will compare the items.

But you have to drag The Corn onto the square thing where the weapon goes, You cant drag it onto where the weapon is on the mech.. If that makes sense..
I dont know, Im bad at explaining stuff o:
and remember, This is all i know, Just experiment with it and you'll get it, I have only done it twice :p

I know ! and Its Me Mechagod