If you needed to lower the saddle, you could remove material from the part of the saddle the contacts the thumb wheels. If there is not sufficient gap between the bridge and the saddle, you could also remove material from the under side of the saddle.
My Eastman AR503CE was setup similarly - not much of a gap between the bridge and the saddle. In my case though, I actually raised the saddle slightly so it hasn't been an issue for me. Was not concerned that the bridge could not be lowered much more than say 1/8" because I figured I could always sand down the saddle if necessary.
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“Sometimes you have to play a long time to be able to play like yourself”
— Miles Davis.
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