No the speedlite won't fully slide in and lock into the hot shoe if its a model with weather sealing. My friend's mom owns the R6 Mark II and her husband owns the R7. The EL-1 won't fully slide in and lock into the hot shoe. The only thing that you would lose functionality wise would be the IR AF Assist Beam. The speedlite will switch to Intermittent Flash Firing (IFF) automatically. Even speedlites such as the EL-1 which has choice between IR and IFF. Will use IFF on the EOS R series. All that setting does if a color filter or flash diffuser is used and the speedlite is set to IFF. The camera body will emit an LED AF Assist Beam. The way how IFF works is the camera rapidly varies the voltage to the speedlite to control the brightness of AF Assist pre-fire.
If you're looking into a new speedlite look into the EL-5 it uses the new multi function hot shoe natively it doesn't use the older 5 pins on the hot shoe. The EL-5 has an LED AF Assist Beam instead of using IFF depending on the camera body.
