For some reason, srwiki uses custom sort order for interwikis. This can be solved by including the following into srwiki's local settings:

$wgWBSettings['sortPrepend'] = array(
'ace', 'kbd', 'af', 'ak', 'als', 'am', 'ang', 'ab', 'ar', 'an', 'arc', 'roa-rup', 'frp', 'arz', 'as', 'ast', 'gn', 'av', 'ay', 'az', 'bjn', 'id', 'ms', 'bg', 'bm', 'zh-min-nan', 'nan', 'map-bms', 'jv', 'su', 'ba', 'be', 'be-x-old', 'bh', 'bcl', 'bi', 'bn', 'bo', 'bar', 'bs', 'bpy', 'br', 'bug', 'bxr', 'ca', 'ceb', 'ch', 'cbk-zam', 'sn', 'tum', 'ny', 'cho', 'chr', 'co', 'cy', 'cv', 'cs', 'da', 'dk', 'pdc', 'de', 'nv', 'dsb', 'na', 'dv', 'dz', 'mh', 'et', 'el', 'eml', 'en', 'myv', 'es', 'eo', 'ext', 'eu', 'ee', 'fa', 'hif', 'fo', 'fr', 'fy', 'ff', 'fur', 'ga', 'gv', 'sm', 'gag', 'gd', 'gl', 'gan', 'ki', 'glk', 'got', 'gu', 'ha', 'hak', 'xal', 'haw', 'he', 'hi', 'ho', 'hsb', 'hr', 'hy', 'io', 'ig', 'ii', 'ilo', 'ia', 'ie', 'iu', 'ik', 'os', 'xh', 'zu', 'is', 'it', 'ja', 'ka', 'kl', 'kr', 'pam', 'krc', 'csb', 'kk', 'kw', 'rw', 'ky', 'mrj', 'rn', 'sw', 'km', 'kn', 'ko', 'kv', 'kg', 'ht', 'ks', 'ku', 'kj', 'lad', 'lbe', 'la', 'ltg', 'lv', 'to', 'lb', 'lez', 'lt', 'lij', 'li', 'ln', 'lo', 'jbo', 'lg', 'lmo', 'hu', 'mk', 'mg', 'mt', 'mi', 'min', 'cdo', 'mwl', 'ml', 'mdf', 'mo', 'mn', 'mr', 'mus', 'my', 'mzn', 'nah', 'fj', 'ne', 'nl', 'nds-nl', 'cr', 'new', 'nap', 'ce', 'frr', 'pih', 'no', 'nb', 'nn', 'nrm', 'nov', 'oc', 'mhr', 'or', 'om', 'ng', 'hz', 'uz', 'pa', 'pfl', 'pag', 'pap', 'koi', 'pi', 'pcd', 'pms', 'nds', 'pnb', 'pl', 'pt', 'pnt', 'ps', 'aa', 'kaa', 'crh', 'ty', 'ksh', 'ro', 'rmy', 'rm', 'qu', 'ru', 'rue', 'sa', 'sah', 'se', 'sg', 'sc', 'sco', 'sd', 'stq', 'st', 'nso', 'tn', 'sq', 'si', 'scn', 'simple', 'ss', 'sk', 'sl', 'cu', 'szl', 'so', 'ckb', 'srn', 'sr', 'sh', 'fi', 'sv', 'ta', 'shi', 'tl', 'kab', 'roa-tara', 'tt', 'te', 'tet', 'th', 'ti', 'vi', 'tg', 'tokipona', 'tp', 'tpi', 'chy', 've', 'tr', 'tk', 'tw', 'udm', 'uk', 'ur', 'ug', 'za', 'vec', 'vep', 'vo', 'fiu-vro', 'wa', 'vls', 'war', 'wo', 'wuu', 'ts', 'xmf', 'yi', 'yo', 'diq', 'zea', 'zh', 'zh-tw', 'zh-cn', 'zh-classical', 'zh-yue', 'bat-smg',
);

Disregard previous comment. I see that srwiki's sorting order is implemented in WB client itself, so it should be just:

$wgWBSettings['sort'] = 'alphabetic_sr';

I don't know how/why it's not working but shall poke at this.

Ultimately, we want to be able to use custom sort orders if they are defined in MediaWiki:Interwiki_config-sorting_order and only have a handful of default sort order settings.

I am having some trouble understanding the issue. Can you please give me a specific wikipedia page, as an example?

I am looking at http://sr.wikipedia.org/wiki/%D0%9F%D0%BE%D1%99%D1%81%D0%BA%D0%B0 which I purged. It has 'bat-smg' last in the sorting, after zh and everything. It is consistent with http://sr.wikipedia.org/wiki/%D0%9C%D0%B5%D0%B4%D0%B8%D1%98%D0%B0%D0%B2%D0%B8%D0%BA%D0%B8:Interwiki_config-sorting_order None of the other sort orders are like that.

Is there something else out of order there?

OK, it appears that the correct order is established after the page is purged. But what cause the wrong order to appear in the first place? Is this a one-time issue or will this happen again whenever Wikidata is updated?

@nikola: I really don't know.... if you see an example where it's not correct, then we can take a look and investigate.

wikiwind / Nikola: Could you provide an example, please?

wikiwind.wikipedia wrote:

http://sr.wikipedia.org/wiki/%D0%9E%D0%BA%D1%81%D0%B8%D0%BC%D0%BE%D1%80%D0%BE%D0%BD

Interwiki links order is wrong, and there is no "edit links" link to wikidata.

This seems to be fixed now. Closing. Please reopen with link to article if it still happens.