This app is not related to the official IOIO codebase. You better contact the author with this question.
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You don't need to upgrade the bootloader, only the application firmware. For your (old) version of the board, this is done using the IOIO manager application, which unfortunately requires you to be using an Android <4.1. This is only a one-time process, you'd be able to use the IOIO with any Android later.
It's all on GitHub. I thought it's been agreed that you can do everything you need with the stock firmware, but up to you...
Alternatively, you can use a v3.x version of IOIOLib.