Like most established development teams we have separate Oracle Instances for different environments (DEV/TST/PRD...). We have Team Coding enabled in all environments above DEV. To move something from a lower environment to a higher one I typically use Object Compare to generate the script, click the button to copy it to an Editor window for the required Connection and execute it using Execute Script (F5) once reviewing it. I have Team Coding set to Prompt for Comments on Check-out and require them for Check-in. If the code modifies an object that is not checked out Toad immediately pops up the Check-out screen and defaults the Comment to "Script objects Added by Team Coding." . I am able to replace that generic Comment with something more meaningful and then select Check-out. Toad then processes all the changes in the script and automatically checks in all objects modified by the script. I have noticed the auto check-in process does not honor comments added during Check-out and overwrites them with the generic comment.
A workaround is to always do a manual check-out, manually execute every SQL statement in the script, then doing a manual check-in. This is very time consuming and it would be much cleaner/more efficient if the automated process would not overwrite comments entered during the check-out phase when it does the check-in.
I found if you do a manual check-out and populate the Team Coding comment, then run the script as a script, Toad automatically checks in the object with a generic comment.