I don't reload shotshells..... yet, so shot hasn't been an issue for me, but powder is easily vacuumed out of the track. If you do spill a lot of shot, I would just run the tracking to the front of the bench. Really, it would have to be completely full for it to be a problem, so I don't think I'd worry about it. I have occasionally dropped a few pieces of stainless media in the tracking and it didn't cause any problems.
I didn't mention it, but you could also run the tracking sideways. If you look at the cabinet/woodworking table ideas, some them even have tracking going both ways. There are lots of interesting ways to make your bench surface modular. I'm sure you will come up with something that works well for your use. Please post up some pictures when you get it put together.
I'm thinking my next setup will be made with a butcher block or old bowling alley lane top and I'll do cork flooring in the room. Led lights will work better with electronic scales than my current overhead florescent setup. Make sure you secure the bench to the studs if you are going to have your scale on the same bench as your press.