This is a well known thing. The loading order under Macs and Windows is alphabetical, while Linux is unpredictable. There is no solution for it yet.
There might be a couple of potential solutions.. the same problem has been encountered with other games on Linux that rely on loading mods in a specific order, and I've found the following workarounds reported as working:
One person created a shim file system created using FUSE
(Filesystem in Userspace) that sorts directories before returning the file list.
This seems less than optimal, as it would require the player to install FUSE, set up the shim filesystem, and (possibly) then set it up to work with Oolite.
Another person used a sorting script to sort files and rewrite them to a USB drive in alphabetical order, to deal with idiosyncrasies of the FAT filesystem on MP3 players.
This does suggest a possible workaround for Oolite on Linux, but it would involve making changes to the core Oolite code.
What would be needed is a pre-loader code section for Linux builds which, before loading the addons, parses the entire OXP/OXZ directory listing into an array, sorts it, and then uses the sorted list to load all the addons in alphabetical order. Such a routine shouldn't be too hard to create. But there may be some 'gotchas' involved.. I've never looked at the addon loader and caching routines in Oolite.