So this looks like if you include a file from Application.cfc, onApplicationStart() won't fire;
(gives application.name="BEFORE", and "foo" is not in the application struct.)
Attempting to run cfWheels 1.4.1 on Lucee Express 5.x (any version).
The key [WHEELS] does not exist, only the following keys are available: [applicationname].
It's as though onApplicationStart() never gets called. Wheels is fine in 4.5.x, so this is a 5.x specific thing.
Steps to reproduce:
Download Express 5.x, unzip https://github.com/cfwheels/cfwheels/archive/master.zip into webroot, startup.
If it helps, the wheels startup/include process is something like this: