I'm working on a theme idea in which I take four theme words that are related, add a second word to make a common phrase in which the meaning of the theme word is changed, then clue it punnily using the theme word's original meaning. For example, RUNIN might be a theme word based on its meaning as "a quarrel", and the entry would be RUNINSIDE clued, perhaps, as [Hatfield or McCoy?] Not what I'm really working on, which I hope is better, so don't get hung up on this entry.
Key point: notice the parsing of IN - it's part of RUNIN in the theme, but part of INSIDE for the more common phrase. I don't have examples to go along with RUNIN, but in what I'm working on the other three theme words don't have this change of parsing; the theme word remains intact when read as the common phrase.
So there's a slight inconsistency in the parsing. But all the entries are consistent wrt the theme - a common phrase contains a theme word and is clued based on that word. The question is - is this inconsistency fatal? Does RUNIN have to get tossed?