When I got my gmax I had the exact same issue. Now that I have the heated bed, the new glass is a little better but not perfect... Its nearly impossible to get something 16x16 perfectly flat... but only .05mm can throw this all off.
A few points.
1. The ABL probe can only measure up to .1mm of variation across the entire surface.... Someone told me that, and if true, thats terrible.
2. Most of the spots that were not level were holes, or "spots" not a consistent corner to corner change. So that means the ABL probe never reached in to those spots when it did its grid. Even at 16 pts it never hit them. So you would have to set up 6-10 probe points to make sure you hit those, and im still not sure it would work.
3. If you set it up to compensate for the depressions you will "smoosh" the rest of the first layer a fair amount, which will look bad, but SHOULD work. It has for me.
4. Raft will work, but I hate using rafts. S3D rafts are terrible, and rarely come off right... They have ackowledged a major issue with their raft settings, but I dont know that its been resolved. I HATE how the bottom layer attached to a raft looks. I need nice clean parts.
5. Upping the layer height for the first layer works to an extent, but getting dialed in higher layer height, with extrusion width, etc etc etc is a nightmare. I spent probably 10 hours trying to get it right and never did. Problem is, if you extrude at .3 or .4mm for the first layer, then inside (the fill) never overlaps and looks terrible etc.
I dont know what the answer is,but ive yet to print 1 large print that covers the majority of the bed, and dont have plans to. However id like to know when the need presents itself I have that option. Right now, I dont feel comfortable doing that.