Right now, and for quite a while, interwiki links on English Wikipedia's Main Page are sorted incorrectly: Bahasa Indonesia and Basa Jawa are sorted under B while they should be under I and J.
It is possible to sort the links manually (at Template:Main Page interwikis), however since the interwiki bots are used very rarely now, this could easily become unsorted again when a new language is added. Then, there is a question of how the links are sorted on other Wikipedias etc.
So, I suggest that alwaysSort option is returned to Wikibase Client, or to introduce a new magic word, for example {{sortinterlanguagelinks}} that would sort the links.