Why did Hunt's team set a 90 seconds limit to take out the tracker from Lane's neck?

I think that 90 seconds is just the amount of time it takes to take out the tracker. The reason they wanted to remove the tracker was to implant their own tracker into Lane. Lane, should he have gotten free, would've removed the tracker himself but now if he were to be freed he wouldn't know that he still had a tracker on him. This new tracker having been put in place by the IMF and not the Parisian authorities that were holding Lane and trying to get him back from Hunt's team making not only Lane but Walker not realizing that Lane was still being tracked.

I also believe they did this in order to set Lane's tracker as visible again and when they set the drone away with Lane's tracker to keep the authorities on a goose chase thinking that Lane was still on the move while Hunt's team escaped with Lane. When they finally set the drone free you can hear helicopters passing by overhead. They drew the authorities closer to the tracker and then set it free instead of them trying to follow them to the sewers.

They set a 90-second time limit to remove the tracker because they knew that was the minimum response time from the secret service.

As you can hear, just after the 90-second mark, the authorities are closing in - so they had correctly evaluated the deadline for transferring the tracker to the Drone and misdirecting them.