Woodbury, Hanni. A Reference Grammar of the Onondaga Language. 2018. hh:g:Woodbury:Onondaga
/kʷ ts/ are "disstinguished symchronically from the otherwise identical sequences /k/+/w/ and /t/+/s/ in only two contexts: (i) at the orpheme boundaries that require e-epenthesis with the latter, but not the former (section 2.6.2), and (ii) in contexts subject to the rule of second-syllable vowel length (section 18.104.22.168) which the internally complex consonants fail to condition without the presence of a second resonant. Thus it is impossible to establish their presence in other environments except by means of comparative evidence."
More allophony: "Words ending in /h/ typically lose it utterance-medially except that some speakers retain word-final utterance-medial /h/ if the following word begins in /n/.2 While underlying /ʔ/ does not occur word-initially, phonetic [ʔ] is added utterance-initially before a vowel and between two words the first of which ends in a vowel and the second begins in a vowel as in degní é·git [degní ʔé·git] 'two acres'. Words ending in a vowel are followed by a phonetic [h] prepausally. "