There is a lot more than just your occasional use of the app that uses the12V -- some you have more direct control over and can minimize, others not as much: Energy Savings and Always Connected On/Off Settings; Possible USB Phantom Playing; Every time you walk by your MS with your FOB and MS senses it opening doors and turning on some lights; Opening/Closing your charging port; Tesla polling your MS to pull up log data or downloading updates of various sort; Some people that inadvertently use computer apps to wake up their MS 7x24 to gather tracking data; and more. If you are doing things like turning on your air conditioning or playing around opening the pano "just because", well, those sort of decisions are of course on you in terms of using the battery.
IMHO, don't get paranoid over how much use of the Tesla App itself even a few times a day may impact your 12V battery -- it's likely minuscule compared to a lot of other things. Take the time to read this whole thread and a lot of others when you have the time to become more informed -- reading only a few posts in many of these threads can send up red alerts to the uninitiated. I've found that perspective counts and helps a lot not going off the deep end trying to do or not do things that just are not that necessary in the larger scheme of things.
Instead, if you've seen "the 12V message" or another one that concerns you, next time, I'd offer its a lot more important to just note the date/time you saw it, then call your Service Center to report it. They can look through your logs to see what's going on, and either reassure you or set up an appointment to resolve whatever it may be.