set myFolder to (path to home folder)
list files myFolder conforming to {"public.folder"} without invisibles
And it would choke SE and SD here too, so I also used Explorer (for lurkers: it lets you limit how many items in a list are logged, hence it doesn't choke in this case).
So here's the start of my log:
0008.958 tell current application to list files alias "Macintosh HD:Users:shane:" conforming to {"public.folder"} without invisibles
--> {file "Macintosh HD:Users:shane:.adobe:", file "Macintosh HD:Users:shane:.android:", file "Macintosh HD:Users:shane:.bash_sessions:", file "Macintosh HD:Users:shane:.CloudStation:", file "Macintosh HD:Users:shane:.CloudStation:db:", file "Macintosh HD:Users:shane:.CloudStation:log:", file "Macintosh HD:Users:shane:.config:"...
All invisible folders.
Hang on -- I wonder if list files is taking only the old Finder invisible flag into account. Could that explain what you see?