You're right, it'll prevent any seeds from germinating not just the weeds. So once your seeds have germinated then you're fine using the pre-emergent. Only catch is, a lot of the weed seeds will probably germinate around the same time as the seeds you're trying to grow before you've been able to use the pre-emergent, so its effectiveness may be limited. But if you tend to get a lot of weed seeds sprouting later in the season then it can still help control the later ones.
I used PREEN heavily every 2 to 3 months this spring primarily because last year's drought brought in a whole lot of weeds during times we had lots and lots of daily wind. I found that it is not 100% effective, and I believe that it can only removed probably 85-90 % of the sprouting weeds at beds. My coneflowers and many other seeded perennials and annuuals DID make seedlings which I transplanted to new locations. I still had to pull weeds regularly, but less than it would have been without PREEN.