I think this is probably more of a question for that vendor than one for the EMM provider since they aren't incrementing their versioning appropriately at compile time. 

Completely agree Matt. Unfortunately I have no control over the vendor and was just looking for a work around. 

I don't think there is any workaround from MobiControl itself as of now.

One possible workaround is to use an app that reads "versionCode" field of all/selected apps installed on the device, and reports the value to MobiControl via custom-data mechanism.  There is probably no such apps currently on the market that does exactly the above, but there are open-source app project can be used as a template/basis to build the required app.  I believe an average Android app programmer can make the required changes in 1-2 days, if not 2-3 hours.

With the custom data (say app123_version_code) collected, the value can be selectively displayed in a custom column alongside other deive attributes in the device view on the web-console.  One can also use Alert rule to trigger different server-side action based on the value of such collected data value.