I think the main Fldigi list would be the best place for this qurstion since it really has nothing to do with the NBEMS type usage of Fldigi.
Anyway, the issue of mismatched emphasis is mostly a matter of the software decoding the signals. In a packet setup using old TNC2 hardware, the mismatch or "twist" really hurt the the decode performance. More modern systems like KPC3s and software TNCs like Direwolf, UZ7HO Soundmodem, etc. all deal with the mismatch pretty well. Generally speaking, all HAMs should use the right configuration but some modern radios do the WRONG thing on the "1200bps" RX pin and TX pin on the rear 6pin "DATA" jack and NOT apply the expected de-emphasis and emphasis! Beware!
So the question of how Fldigi deals with it will generally depend on the modes you're using. The potential risk I see is a remote station transmitting via the 6pin discriminator input at maximum levels and then a local station applying de-emphasis on the signal and lowering the high frequency levels by ~6dB.
The wider the bandwidth, the more potential impact there might be. I bet that the Fldigi modem will deal with the different levels just fine.