1. The presence of the lift kit should not be a problem as long as your hitch-height can be adjusted high enough to provide for ~level trailer when towing. See the current
5.0 Towing Compatibility Guide for hitch height info.
2. Though ETI doesn't want to provide the accommodation, IF they are still using the bolt-on lift kit that was common through mid 2022 then any competent mechanic (perhaps you?) can remove that lift-kit (essentially a bolt-in spacer block) after you take delivery. ETI should be willing to at least confirm that the 2023 lift kit is still a bolt-in spacer block type.
This webpage shows the lift-kit parts used by ETI for trailers up through at least mid 2022 along with written and video installation instructions; removal is simply the reverse:
Torflex Lift Kit for #10 axles on eTrailer.com
3. IMO generous bed-rail clearance can be a blessing on some ocassions.