I used to have my large bases spawn on the flattest areas of the map with the max elevation set specifically for those profiles.  With the new update, I've had to disable those profiles due to the max elevation being globally applied in the config folder.  Higher elevations cause these larger bases to anchor at one end and leave the other end the in the air due to terrain.  Am I missing something or is this the way forward with elevation settings?  

yes this is how it will be done now. you certainly should be able to use 2.0 or 2.5 elevation for all bases regardless of size

I had a similar problem when I upgraded. Re-paste and save the larger bases causing you problems.

Enter the base and look at the lowest foundation while saving. Then set the paste options in the profile to this "Option": "height", "Value": "1.0" and let the pluging do the work. So Far appears to have 99 percent resolved my problems.