If you have a Nano or an iPod Touch with 30 pin connector, it should fit in the Go-Dap 3 without any modification. I've used the Go-Dap 3 with the first- and third-generation Nanos no problem, along with the 3rd Gen Touch. All of them need some kind of material behind them to keep them secure and fill in the space somewhat. VentureCraft "unofficially" suggests some cloth, IIRC.
The idea of removing some of the plastic to allow this amp to be more "universal" is interesting. I would be curious if anyone figures out how to dock the unit with a 30-pin iPad without any additional cable. Another possibility might be the iPod Classic, but I think the dock connector might be too close to the amp back even if some plastic is removed.
Using this amp with a 30-pin extender cable works fine.