If I installed my app on system and Enrolls as Device Owner at setup
Blocks factory reset via DevicePolicyManager restrictions (DISALLOW_FACTORY_RESET)
Disables USB debugging (DISALLOW_DEBUGGING_FEATURES)
Would my app survive manual wipe
Why would it? DISALLOW_FACTORY_RESET only disable factory reset from the setting, the device itself should still be able to enter recovery mode to wipe everything in user partition, including your app.
If you mean your app is installed in the system partition (which imply root, or the ROM is customized), then factory reset won't affect it.