The denomation question could be important, as if it's the Skehan family that where Church of Ireland it changes the parishes you need to look out for, and since Charles and the children are listed as RC it's sounding as though that's possible.
Carrick on Suir is some distance from where the couple married, and marriages tend to be in the bride's current parish... sounds more like Cahir was the current parish for Charles, or did Mary originally come from Cahir, but was living near Carrick-on-Suir at the time but returned to Cahir for the marriage ?
RC records for Carrick-on-Suir for back to the 1780s, and transcripts are on RootsIreland paywebsite, but as I'm sure you've already seen there's no good match for Mary in these. Carrickbeg records which cover the south of the town are also included, and dont show a match either. RootsIreland dont seem to have CofI baptisms for Carrick-on-Suir.
Is the bride's residence clear to read on the cert ?
There are several townlands named Knockroe in Co. Tipperary, and Co. Waterford (parts of which would be close to Carrick), and there could be more as variations of spelling, but none that I've been able to find that seem to be near Carrick-on-Suir. There is a Knockroe in Clogheen district, Neddans civil parish so could be close to Cahir...
It's a pity they just seem to have missed the 1891 English census - that might have helped with a county for Mary
p.s. long shot ... on the basis that Knockroe might a mishearing or similar or difficult to read and actually be someplace that reads or sounds similar I checked for any townland names where the name starts with "Knock" and in Carrick on Suir poor law union, so likely close to the town. Just one townland matches - a Knocknaconnery, which not only is in Carrick on Suir poor law union, it's in Carrick civil parish, the same as the town. The first name that shows up on Griffith's search for this townland is a 'James Skeahan', and he's listed as occupier in the townland with a house, offices (i.e. stables, workshops etc) and land of just over 27 aces. He's a tenant of a Rev. Francis Brisoce, and this section of the valuation is dated 1850. Knocknaconnery townland is located just north east of the town of Carrick on Suir...