Giving function arguments in templates
I would recommend looking at Module:sl-headword. Slovene has no transliterations, but many other aspects, such as the need to always provide an accented headword, are the same. I wrote the module some time ago and would probably do some things different now, but it's a start. I may actually bring it up to standard soon, and then you can take your code from it and adapt it to Serbo-Croatian.
Because we need it done in the headword, and we need to transliterate in both directions, reworking {{head}} to handle this with through its normal transliteration mechanisms would be impractical.
As for writing the module, I just want it to function the same as the old template system for now, until we figure out what inflectional information we want to require in the headword.
The concrete problem I have is why {{User:Crom daba/sh-noun|head=gòblēn}}, which is defined as {{#invoke:User:Crom_daba/sh-headword|head_t|nouns}}, won't function the same as {{User:Crom daba/sh-head|nouns|head=head=gòblēn}} but rather as {{User:Crom daba/sh-head|head=head=gòblēn}}.