Hi, andyj!
I didn't knew, that this /usr/local/etc/X.d chain in .xsession is Your contribution :-) Great thing, surely! It was added not long ago and that is why it is not widely used by maintainers, I think it needs to be promoted, but I don't know how - wiki is down :-( I must say, that some topics were dedicated exactly to troubles, which could be cured using this per-extension X startup scripts. One of the examples is terminus-fonts.tcz, I use it every day and it needs manually created script in ~/.X.d, however this manual action could be avoided by adding corresponding /usr/local/etc/X.d script to the extension. If I am not mistaken, /usr/local/etc/X.d is the right place for all the fonts caching calls. Probably there are another common cases for this directory use.
Of course I realize, that /usr/local/etc/X.d scripts will be executed only at X startup. I was mentioning that their invocation order (at X startup) will be the reverse load order in onboot.lst, because their links are created inside /usr/local/etc/X.d during tce-load and consequent "find ... " (in .xsession) will list them in reverse creation order. Maybe it is filesystem dependent behaviour, I'm using ext4 and didn't tested the others.
Regards!