Cranksets that utilize external BB bearings are 2pc designs. The spindle is pressed into the back of the driveside crank arm; there is no separate spindle to worry about. On a 2pc road crank (e.g., Shimano Ultegra 6700), the spindle is just long enough to accommodate either English (68mm) or Italian (70) road frames. On a 2pc mountain crank (e.g., Deore), the spindle is wide enough for 73mm BB shells, since this is the modern standard for MTB frames. If you're installing a Deore Hollowtech crankset onto a 68mm BB shell, you install the additional spacers that are included with the crankset; these slip right onto the spindle between each crank arm and each bearing. So rather than installing just one 2.5mm spacer under the non-driveside crank arm, you would install two 2.5mm spacers under the non-driveside arm and another 2.5 spacer under the driveside arm.

Mountain bike cranksets typically mean you have a wider "Q-factor" than on road cranks. This is where some people see an advantage with square taper cranks, since you are free to use a narrower spindle to get a narrower q-factor. That option isn't available when the spindle is pressed into the right crank arm. The difference isn't especially great and shouldn't be annoying unless you're particularly sensitive. There's also the chance that the q-factor of a Deore wouldn't be any greater than the Acera you currently have.