I did a little testing with #onebattlespell. I think I have found a decent way to use it without it wrecking mods.
I chose a null spell number (87) and used #selectspell 87 to create the spell I wanted to use for #onebattlespell.
Instead of creating new spells, using selectspell should do the job nicely. If you cannot do a #selectspell 829 etc etc without a spell being created, you could create a mod that creates a bunch of blank spells (829 through whatever) then just use select spell for all your custom #onebattlespell needs. If you made say 300 dummy spells, then you could do a #selectspell 1000 (well out of the range new dev spells will be added I imagine)and use it for your new #onebattlespell.
Another important thing to remember about #onebattlespell is that it allows that caster to cast the spell as if it were researched. This means that a caster may potentially spam the spell you wanted cast one time.
The spell I wanted my commander to cast is a spell I did not want as a true national spell so I fixed this by setting the fatigue to 5000 and setting it to -1 for a school. The spell does not appear in the spell books and my commander casts it one time at the beginning of battle, just like I wanted
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I tested with 2 #onebattlespell on one commander. The mod loads fine but the commander will not cast either spell, so you can't assign a commander to put on a magic show at the beginning of a fight
