The RTCM is totally flexible regarding emphasis. Although the way it is set is completely obscure. It tries to automatically do the right thing for you, which is great most of the time. But when it’s not it's hard to know what is going on.
On the TX side the RTCM expects the repeater to accept mic audio. In other words, the repeater is providing the pre-empahais, not the RTCM. This can overridden by setting CTCSS on in voter.conf in which case the RTCM will provide pre-emphasis. If you don’t want TX CTCSS but do need pre-emphasis set the level to 1 which is low enough that it won’t be there.
On the RX side the COR Type setting determine the emphasis. 0=Normal means the RTCM squelch circuit is in use and expects discriminator audio, therefore will provide de-emphasis. 1=IGNORE COR uses the CTCSS input for COR (+CTSCC) and expects line audio, therefore will not provide de-emphasis.