As far as I know it doesn't make any difference. I've done them both ways (before and after the bulb). To my knowledge, never a problem. Sometimes packaging constraints get in the way and we just had to make it work whichever way we could.
Nowdays some of the outboard manufacturers will not allow a seller to register the warranty until the filter/separator has been installed, among other things. I know we have to check the box that says "filter/sep installed" on the pre-delivery inspection forms, and the forms have to be submitted before they'll register it properly. They're getting pretty strict on fuel delivery stuff with all the sub-par fuel blends coming to the market.