I agree that it's in bad form to use less clear on a standard game that costs the same amount as the LE even though at this point we don't really know what the difference looks or plays like.
The standard version with less clear probably plays more like an original MM since WPC games aren't known to have super thick clear on them like restored games do. I actually prefer the way original playfields play vs. restored as a super thick/hard clear plays too fast and the ball seems to skip around too much. I'm also not sure that the extra clear is really necessary to protect a game that is in a home use environment, especially since everyone will likely install cliffys and other protectors on their game.
The cosmetic differences (shaker,trim, plaque) are enough to differentiate the two games. Once you start changing the way the two games play by making them faster or slower, I think you've gone too far.