User blog comment:Gilgameshkun/Mirage TMNT transcripts dilemma/@comment-93957-20180407003703/@comment-995426-20180407013154

Two guides...that can certainly be done. I designed Template:TranscriptNav to be flexible to allow for that. (And Template:IDWTranscriptNav just uses the other one.)

And yeah, outside Tales, publishing order for the most part does establish chronology, though even then there's a few exceptions. For example, #27: Dreams of Stone takes place after #28: Sons of the Silent Age, not before it.