It is not the FastATA which takes ages, it is the onboard IDE on the motherboard. As long as there is any kind of drive attached to it, it will boot quickly but if there is no drive connected, the Kickstart will wait up to 30 seconds before it boots from another controller.
There is a hardware hack which solves this on Aminet. IIRC it is called IDE-Killer or similar.
The FastATA might speed up things a little. But it is not the raw transfer rate which makes the system fast. You should first consider replacing the file system by PFS3 or SFS before you decide to buy a new controller. Because optimising seek accesses will improve the speed more than increasing the transfer rate.
And of course the FastATA does not use DMA either, so you should have a fast processor (68060 recommended), too.
The best advantage of the FastATA is that its firmware supports 64 bit commands out of the box. So with an adequate file system (SFS, PFS3, FFS V43+) you are able to handle HDDs bigger than 4GB without any patch and no additional reset is needed.
Bye,
Thomas