If you have to convert the audio track, you should fix the delay. This way the problem is definitely fixed and if you have to use again these streams for whatever reason, you won't have to think about it again.
If you don't have to convert it, then all depend of the tool you use. DVDLabo Pro does not fix the delay, it includes a tool that does it. Some tools like mplex manage the delay directly at the multiplex level.
I prefer to fix it before to load the authoring tool for the reason explained above.
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