Don't worry, time coded lyrics and midi messages, along with midi clock, will not interfere. Doesn't matter where in the lyrics you put midi messages to change presets/lights. I programmed ST3 to change presets and settings on 2 synthesizers (WIDI Master) and 1 vocal processor (by 5-pin midi cable from audio interface) with time coded messages and midi clock (helps with time-based effects). It is just easier to manage all messages at the beginning of a song.
My advise is to put annotations what each midi command is supposed to do. On a new line type ; and then a simple explanation. That way it will help you understand months later what exactly you programmed. If a line starts with ; it will not show up when the song is playing. It shows only in the lyrics editor.
Good luck!