I came across an old posting of yours on Amibay regarding this matter. A quick test with an NTSC Agnus (390544-02) is indeed causing the startup animation to lock up, but I have good hopes that the anim can be bypassed. The 28.6363 MHz oscillator is only useful for genlocking and since the GBA's RGB port is missing some essential genlock signals (particularly /XCLK and /XCLKEN), this is not much of an issue anyway. I cannot confirm your IDE performance drop.
Jiri sent me another nice photo of his GBA, with the Picasso II and the 68060 turbo card removed for the occasion.