I've installed my Indy Mk2 in a Commodore 1D4 A1200, left away the metal shielding completely. The Amiga uses an 8GB CF-Card via short-wired adapter to the internal IDE. It is powered by a Blizzard 1230 with SCSI-Kit installed (used only for memory expansion). I don't experience any kind of glitches even after hours of running in Workbench mode 1024x768.
I don't know at all why my Amiga does not show any problems at all.