RAM gets checked and verified during the power-up boot cycle, so more RAM in the iMac will add a couple seconds to the boot process compared to the MacBook.
A Fusion drive will be slower than an SSD, regardless of where the OS resides. The OS will have to wait for the mechanical portion of the Fusion drive to report itself ready (spin up to proper RPM, etc.). And there may be files, however small, that reside on the mechanical portion of the volume that the OS will have to wait extra time to access. Not likely to be 3 seconds worth, but even just a half second is still 1/6th of the time difference we're looking at in this example.
Additional login items, as others have mentioned, could also add a small amount of time to the boot process if each Mac isn't set up the exact same way. Even system hardware drivers (like a Logitech mouse driver, etc.) that one Mac has that the other doesn't can add a fraction of a second, which in this case, can make a detectable difference.
Additionally, what are the CPU speeds of your two Macs? If the MacBook Pro is a Core i7 and the iMac is a Core i5, that could potentially explain some bit of difference, too.
Add all these fractions of a second up and you could easily get to the ~3000 msec difference you claim.
Bottom line: the difference you see is insignificant.