I'm guessing it's because even if you use it instantaneously after drinking a 60 second long potion, you're technically drinking it at 59 and 19/20ths of a second remaining. However, I've noticed that with longer potions after the potion filter is "locked" to them you can occasionally get their full duration (ex. 1 min 30 second potion adds 90 full seconds to the potion filter) when holding the filter in your offhand and continuing to hold right-click after drinking the potion. This behavior seems somewhat inconsistent to me.

Would it be possible to give a tiny bit of leniency to the potion filter to allow 60 second long potions to be used?

You can adjust the time in the config for this. Technically, the time being added to the card is counted in ticks, rather than in seconds. So what you are probably seeing with the 90 second potions is that there are a couple ticks left over from the previous potion, and then when you add the next potion it's added together to make up a full second.