Regarding the superscript q, in some rare cases, it is used to indicate pharyngealization or a pharyngeal consonant instead of the Latin letter pharyngeal voiced fricative U+0295 ʕ, the modifier letter reversed glottal stop U+02C1 ˁ or the modifier letter small reversed glottal stop U+02E4 ˤ.
Menán du Plessis uses a modifier letter small q after a vowel in ǀXam to indicate pharyngealization of that vowel in a few papers (Notes on Qings own languages <https://www.academia.edu/21215819/Notes_on_Qings_own_language>, A century of the Specimens of Bushman Folklore <https://www.academia.edu/7450999/A_century_of_the_Specimens_of_Bushman_Folklore_-_a_hundred_years_of_linguistic_neglect>, A unity hypothesis for the Southern African Khoesan languages <https://open.uct.ac.za/bitstream/handle/11427/11852/thesis_hum_2009_du_plesis_m.pdf?sequence=1> ). A superscript q is also used in the name of the Mquqᵂin/Brooks Peninsula Provincial Park by the Ministry of Environment of British Columbia on the dedicated page on its website <http://www.env.gov.bc.ca/bcparks/explore/parkpgs/brooks_peninsula/> and by the Minister of the Aboriginal Affairs and Northern Development Canada, British Columbia Ministry of Aboriginal Relations and Reconciliation, and the Maa-nulth First Nations in Maa-nulth First Nations Final Agreement <http://www2.gov.bc.ca/assets/gov/environment/natural-resource-stewardship/consulting-with-first-nations/agreements/maanulth2011-2012-implementation_report-dec_17_2013.pdf>Implementation Report / 2011-2012 <http://www2.gov.bc.ca/assets/gov/environment/natural-resource-stewardship/consulting-with-first-nations/agreements/maanulth2011-2012-implementation_report-dec_17_2013.pdf> and 2012-2013 <http://www2.gov.bc.ca/assets/gov/environment/natural-resource-stewardship/consulting-with-first-nations/agreements/annual_report_-_maa-nulth.pdf> . Given the references on the Nuu-Chah-Nulth orthography that are online, it seems the superscript q is used instead of the standard orthography’s Latin letter pharyngeal voiced fricative U+0295 ʕ in the transcription Mquqᵂin.