When upgrading from a Claris to an Ultegra crank, the latter has a gap between BB and crankarm

Some Hollowtech II cranks have a spacer that's supposed to go under the left crank. You need to find the exploded view diagram for your crank model to confirm this. Here's the one for FC-6703 for example, the triple crank for the second generation of Ultegra ten.

If you don't have it, it will probably be okay because these spacers don't interact with the seals in any particularly important way, although they do act as a sort of shield for the seal area to a limited extent. You do need something in its place though, or else you won't be able to preload the bearings. If this is the kind of seal you're missing, the simple thing to do would be get a bunch of scuff washers or whatever other tuneable stack of 24mm spindle spacers you can get your hands on. The nature of Hollowtech II is that as long as the spline engagement is complete give or take some very small amount, the exact dimension of the distance between the cranks doesn't really matter, so you're free in this case to just find something that takes up the gap.