If the time signature change is only occasional (the odd fill, or just the one bar or so), the 'Reset' button on your arranger can be used (sometimes you can put it to a footswitch - even better!) as long as you practice your timing (it doesn't lock to tempo, you HAVE to be precise).
For instance, if you have a 3/4 bar during a 4/4 pice, hit the 'reset' on 'four' and it's now 'one'. It seems tough at first, but practice it and it soon gets easier.
If the odd meter is repeating (Greek music, anyone?!) your arranger can have odd meter time signatures (or at least, SOME can), so if you perform a LOT of these, making sure your arranger has flexible time signature options would be important...
Or.... if none of these options is doable, sure, go ahead and make an SMF of the song. Once again, some recent arrangers allow you to drop in 'markers' for different sections of the SMF, so you aren't stuck with the same length and structure EVERY time you play it!
Also, several different arrangers allow you to go seamlessly from arranger play to SMF play and back, so perhaps create a short SMF of the weird time signature part of the song, play the rest in arranger mode, then hit 'play' on the sequencer for the odd meter section, and go back to arranger mode for the rest....
Plenty of options... You just have to decide which works 'best' for you...
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An arranger is just a tool. What matters is what you build with it..!