Cognate currently can't connect pages in custom namespaces that have different IDs on different wikis.
Wikidata doesn't care at all, I don't see how it is involved in the issue at all.

Indeed, Cognate can not deal with custom namespaces.
This will likely need an extra db table for the mappings of namespaces / ids between wikis.

Hey, I added another special cases: the pages about a punctuation character https://en.wiktionary.org/wiki/Unsupported_titles/Colon

English Wiktionary "Citations" namespace is the same name as Portuguese Wiktionary "Citações" namespace. They are guaranteed to have the same as the current entry (and technically all entries may have a page in that namespace), so I'm guessing maybe Cognate could do the work of linking them.

For example, these two pages could be linked by Cognate:

https://en.wiktionary.org/wiki/Citations:trabalho
https://pt.wiktionary.org/wiki/Cita%C3%A7%C3%B5es:trabalho