How to configure autofs5 timeout on per-filesystem basis?

Edit: the rest of my answer is mostly off-topic. You're doing it the right way, but the feature was only introduced in autofs 5.0.6. From the git repository:

Author: Ian Kent Date: Fri May 25 12:28:56 2012 +0800

autofs-5.0.6 - move timeout to map_source

Move the map entry timeout field from "struct autofs_point" to
"struct map_source".

The result of this change is that an individual timeout may be
set for each direct map master map entry.

Unfortunately only maps can have a custom timeout (overwriting the automount(8) one using --timeout), not entries themselves.

This limitation goes down as low as the Linux kernel itself, which only offers an AUTOFS_DEV_IOCTL_TIMEOUT_CMD ioctl per autofs filesystem, applied on all its mounts. You can find more information in Documentation/filesystems/autofs4-mount-control.txt in the kernel sources.

The best solution I can suggest is to split your entries by timeout into separate maps. This unfortunately means that you'll have different parent directories for your mounts.

If that's a big problem, you could look into UnionFS or similar, but there is no such feature in the official Linux kernel.