Yes, good question about liners sitting proud of cylinder deck.
Mine sit partially proud, partially even and partially sunken in a cyl block.
Next time I take my cyl head off I am going to machine cylinder block to get an even surface and will use Cometic gasket
I'm using now because it holds the top end better than composite or copper. Without machining I still can feel some blowby
on the left ( primary ) side of the head.
I didn't glue my pushrod seals and oil is leaking like crazy from all of them, however I tried to get a proper crush for every
After few good trashings they started leaking, so the next top end service will consist of cylinder block machining, new Cometic
cylinder and head gaskets and covseal gaskets for rocker boxes which by the way are doweled in cyl head.