scripts: gen_handles.py: remove size restrictions

With `gen_handles.py` now running on the first pre-built image,
`zephyr_pre0.elf` there is no requirement for the device handle arrays
to remain the same size after processing.

Remove the padding generated in `gen_handles.py`, as well as the
temporary option `CONFIG_DEVICE_HANDLE_PADDING` which was added to work
around this issue.

Signed-off-by: Jordan Yates <jordan.yates@data61.csiro.au>