I use a light-cured bonding agent for cementing all-ceramic inlays, which I light-cure before cementation. Sometimes the restorations do not seat like they did before the bonding agent was applied. Is it the thickness of the bonding agent? Is it pooling?

Probably the main reason you are having this problem is the fact that you are light-curing your bonding agent before cementation. There is always the potential for the adhesive to pool in corners. Some adhesives have a glass filler, but that is probably not the reason you are finding your restorations not fully seated. It is most likely due to some sort of pooling with the light-cured bonding agent. My suggestion would be to use a dual-cured adhesive that you don’t need to cure before seating your cemented restoration.