I think the purpose of the lifts in the inserts is to allow a bowler to get more revs on the ball.
Most bowlers find a style of insert that they prefer and use it in all of their balls. Some of us prefer a certain style because they feel more comfortable. Others will sacrifice comfort, at least temporarily until they get used to the inserts, for an edge in performance. In your case I would change them to the same as you have in your Path ball.
Having the thumb hole drilled a bit deeper shouldn't have a noticeable effect on the ball reaction.
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