From my point of view this should not matter at all. This part of DB has almost no relation to real biology anyway.
I just have one comment: it should be done in a way that still allows junk DNA. The way I see it, the system should work like this:
we have a "gene execution" flag that can be set to 0, +1, or -1
true condition sets the flag to +1
false condition sets the flag to -1
- when flag is set to +1, program scans for first available "start" and executes the gene, flag is set to 0
- when flag is set to -1, program scans for first available "else" and executes commands after it, then sets flag to 0
- when flag is set to 0, program does not execute neither "start" nor "else", just scans for the next "condition"
This way we can have "cond", "start" and "else" parts in any order we want. The whole deal with "bursting babies when stop is missing" should be removed by the way (or addressed in some way)