We currently can't run configure / cmake on the top-level qt5.git repo when cross-compiling in Coin because that would first require building the host configuration, and we don't usually build anything in the CI for top-level qt5.git configurations, we just run cmake without running make. One exception where we do build qt5.git repo is the documentation configuration, but that's a separate thing.
One solution would be to wait for https://bugreports.qt.io/browse/COIN-553 to be deployed into Coin production, and then perhaps specify dependent configurations, but that still might not be possible because it still means building qt5.git host configurations.
So if we want to test such cross-compiling top level configurations, we might have to bite the bullet and actually build the host top-level build. https://bugreports.qt.io/browse/COIN-553 would at least help in the sense that we can re-use cached qt5.git builds.