The leveling sequence is made when the nozzle hits the bed surface. It doesn't matter what it hits, glass, metal, plastic print surface. This is a classic case of not understanding the different models of makerbot and how they function. Yes, OLDER printers before the 5th generation series used a mechanical limit switch attached to the frame of the printer and hit by the mechanical Z stage moving up and down. The bed and whatever surface was on it had adjustable threaded posts and nuts that the user adjusted to move the bed surface in relation to the underlying mechanical Z stage frame. 5th generation machines DO NOT have limit switches anywhere on the frame.
"when it goes through the leveling process it will hit that glass???" Answer, YES, it will hit the glass- intentionally because that's how it properly works in this series of printer.
This is a function of the MakerBot 5th generation printers including the newer plus.
The smart extruder nozzle can move and is spring loaded to the down position. When your print starts, the printer raises the bed surface until the nozzle hits the little metal inserts in the stock plastic bed surface. The Smart extruder internally senses when that nozzle is pushed up by the bed contact. The idea was that the little metal inserts in the stock bed are level or very near level with the plastic print surface. When you add a glass plate to 5th generation printer now the hard glass surface IS the same point the nozzle hits. The main reason for the metal inserts was to keep the hot nozzle from melting a hole in the same spot of the stock plastic surface. Further, the previous model of 5th gen printer came from the factory with a glass bed surface and STILL used the same basic smart extruder Z homing method.
What you may have to adjust is the Z axis homing offset. That value is what determines the nozzle height for first layer will be compared to the touch point sensed during the homing sequence.
https://support.makerbot.com/learn/makerbot-replicatorplus/printer-tips/adjusting-the-z-axis-offset_13544