As I understand it, the formula will override the checkmark. But, in cases where the formula cannot be applied, the checkmark or lack of it becomes the default condition. Specifically, there is a difference if you are using the next or previous function and there is no next or previous record.
For example, if you have a checkmark for detail suppression, then the first record will not appear if you use a formula like:
{table.clientID} = previous({table.clientID})
If you uncheck it, the first record appears. You could also leave the box checked and change the formula to correct for this problem:
Not onfirstrecord and
{table.clientID} = previous({table.clientID})
Since discovering this difference, I tend to NOT check the box, but just enter the simpler conditional formula. I'm not sure how this applies to other formatting, but I would think that the "default" condition (checkmark or not) could have an impact whenever a formula can't execute for whatever reason.
-LB