The Apple adapter will not charge the iPad when an iTwo or iOne is connected. It will, however, slow down the pace at which the battery is reduced and should provide enough time for most recording projects.
We've done recordings with the Apple 12W adapter and an iTwo with 2 Mics for 3+ and 4+ hour recording sessions without issue on an iPad without issue. However we did optimize the iPad to accomplish this performance. After testing a brand-new iPad Mini 4 (12W Apple power, iOS 10.3.1, Garage Band running) with an iTwo, the battery life is depleted with or without airplane mode active. After 2-hours, the battery has gone from 100% to 73%.
The power draw of an iOne or iTwo may be aggravating other apps that are already pulling data which requires power to operate in the background.
Take a look at what other applications you may have running that are already pulling / sending data in the background, apps like Skype, or any number of free games that may be installed, or any (free?) game. Even while the iPad is idle and the applications are merely installed and not running, they are still sharing your computing power via your wi-fi connection.
For best performance for running any audio app on iPad with iTwo, iOne (or anyone's interface for that matter with an iPad) would be recommending to enable Airplane mode and dulling the brightness as needed.
This will ensure top performance for your audio project especially if you're running on a battery pack or in an area where reliable power is questionable.