Hi @nickdolling ,
Regarding the issue 1 - changing output path - in the latest recently released version of Config Tools (V12) it's possible to override the path of the the generated files, so it should be possible to use the solution with the multiple .mex files.
To modify the path in the particular mex file, use the Edit -> Configuration Preferences command and there is Output path overrides section:

There you can Edit the set of rules that override the paths.
You can add for example a rule as the following one, that overrides the folder 'board/' in the paths to some relative path "../my_board_folder/" (you can tweak it as you need):

Now all the files that normally go to board folder will go to the one you specify. If you'd like you can create different individual rules for individual files like pin_mux.c etc.
Just please note that having multiple .mex in one folder would now work properly only in standalone version of the Config Tools. It would not work in MCUXpresso IDE, where is expected to have one .mex file in the root of the project.
Regarding point 2 - having multiple labels - it's possible to have multiple labels in the labels field separated by for example '/' character and also multiple identifiers and when you route the pins in the individual functinal group, you can select which labels you'd like to use.
If you'd like to have additional information like (for example additional custom labels or features of pins) stored directly in the tool, there may be useful other new feature from Config Tools V12. You can create a completely customized user signals table, using the new External Signals View.
You can open it using View > External User signals. There you can add list of signals on your board, specify their connection to the processor and add columns with your information on the signals/pins.

Once the connection is specified, the tooltips show the information and state of the pisn and pins are highlighted in Package and Pins view. This table can also be imported and exported using .csv format (editable for example in MS Excel).
best regards
Petr Hradsky
Config Tools Team