Hi,
Clip gain is exported with stems as is automation. If you don't want automation to be captured switch the automated tracks and/or automated plugins automation mode to "Off".
As related to clip gain, that can be reset globally if you want by selecting all clips and CTL+Clicking the gain handle on any clip. In your case you should select all audio tracks and "Duplicate Layer" then reset clip gain before export stems, to still have all of the original clip gain edits on inactive layers.