That's what I did, basically giving myself 1/4" to span with silicone. What happened in reality though, is the glass shop could not make the cuts accurately, and there were some areas that were more narrow than I wanted them. But it turned out to be OK - the silicone was able to span the gaps with no problems.
I used acrylic for mine, so I was able to measure it myself to make sure it fit right.
One think to keep in mind is the bottom of the sump. Mine has a bead of silicone around it, so I cut the corners of the baffles at a 45* angle to account for it. That allowed the baffle to be flat across the bottom.