We operate on QFE on main alts, with standby set to QNH, below transition. We also have the advantage that our Pro-line 21 displays metres alongside feet when selected.
As an aside, the AIP for Russia requires you to operate QFE below transition, within I think about 25 miles of the field. Our company policy is to comply with this, the only exception being in the event of very low QFE.
Our EGPWS does not have any problems with this. Daylight, VMC, absolutely sure that there is no hazard, we may continue with a "terrain" call - a "whoop, whoop, pull up" is mandatory response for us.
Simple and straightforward. If you cannot display meters on your altimeter, then you will need to convert. I have a very nice, one-page conversion table with all the necessary numbers you'll likely ever need when operating in Russia, Ukraine, etc. PM me and I'll send it to you by email. I keep a copy with me all the time, in case my Pro-Line 21 goes TU on me. I also have one for flying in China and would be happy to share that as well.
Keith