As the subject says, starting from Qt 5.9.1 the build system does not pick up the system at-spi2 (changed in 98057fc6c5455c82844a53b374994c33ee1c1a0e in qtbase) and does not build it.
The reason is that there is no at-spi2 configuration option, so it cannot be properly built at all.
The error message given at configuration is also misleading:
"Note: Disabling Linux Accessibility Bridge: D-Bus is missing."
while it's not related to D-Bus at all.
In the source:
"condition": "features.accessibility && features.xcb && features.dbus && config.atspi"
should probably be
"condition": "features.accessibility && features.xcb && features.dbus && libs.atspi"
In fact, doing so allows building at-spi2 support.