They flag "sideloading" - or anything installed by anything outside of their store.

They don't always flag it. Only when SafeNet is set to paranoid levels. However, sideloading is considered a risk for some reason. Even if sideloading is a synonym for "installing".

What if you install the app via adb install? That would flag all developers' phones so I'm almost sure it's not flagged.

Dev mode flags at paranoid level, so I'm almost certain it would.

The developers of this app would have it turned off during debug builds, and on during release, so would be fine.