file(GENERATE): Create output file structures for all directories first

Since commit 36ded610 (PCH: Generate sources during Compute step,
2019-10-05, v3.16.0-rc1~2^2) the source file lookup is done earlier than
before.  Its parent commit f1fb63b3 (file(GENERATE): Create output
file structures even earlier, 2019-10-07, v3.16.0-rc1~2^2~1) prepared
for that.  However, that commit did not account for generating and
using files in separate subdirectories.

Fix this by evaluating all generated files before adding automatic
files.

Fixes: #21144