It will work, but it will be less efficient; "use google libraries" will offload requests for individual JS-files to Google, but those requests remain. Autoptimize's goal is to aggregate as many JS-files as possible, to have less requests, but it will only act on local files.
As an example, suppose you have a site with 10 local javascript files. In that case;
* using Google Libraries you would have 10 requests, e.g. 6 local and 4 offloaded to Google
* using Autoptimize you would have 2 requests, e.g. 1 aggregated JS-file and one file you had to exclude from aggregation
* using Google Libraries and Autoptimize, you would have 6 requests, 1 aggregated JS-file, 1 file excluded from aggregation and 4 offloaded to Google.
Now it would take testing (on webpagetest.org) to see what solution performs best, but my money would we on the Autoptimize-only solution, as extra requests tend to be more costly, even if to Google.
Hope this helps,
frank