First one -- lets you enter a custom mail check interval, such as "4 minutes 45 seconds" -- if the list of "standard" mail check intervals is not flexible enough for your needs / wants (e.g. 5 minutes / 10 minutes / 15 minutes etc).
Second -- the "zero point" for mail check times. For example:
"Reference" = 00:00, and "every 15 minutes" -> 00:00, 00:15, 00:30, 00:45, 01:00, 01:15...
"Reference" = 00:05, and "every 15 minutes" -> 00:05, 00:20, 00:35, 00:50, 01:05, 01:20...
Three -- for when you use apps that turn WiFi and mobile data off and on... lets you add a small delay before AquaMail checks mail, giving network connectivity time to actually connect.