5V 5A rail controlled by 3.3v microcontroller - dual switching or power mosfet?
You will need to compare the current draw of the 5V regulator with a light load vs. the smaller 3.3V switching (or even linear) regulator. Chances are it will draw a fair bit more current. This is your trade-off to make. Remember that when the big print says 86% or whatever efficiency that is the highest efficiency point of operation. The efficiency will go to zero at zero output current and may be worse than even a linear regulator at relatively high output currents (less than ~50mA in some cases for something with several amperes output capability). 

You are going to need high current switching regulation anyway so I wouldn't worry too much about any EMC differences. The 5A will be where the issues (if any) will tend to arise. 

You will probably require a high-side switch for the 5V/5A if you can't control the regulator directly. That is most simply done with a level shifting transistor (from 3.3V to 5V) plus a power MOSFET. Something like a Diodes DMP2006UFG-7 has maximum 5.5m\$\Omega\$ Rds(on) with 4.5V drive would be okay for a high-side pass transistor. That's less than 150mW dissipation. Of course if you can use the regulator control line directly and meet your specifications it's worth avoiding extra parts. If the regulator will accept a TTL compatible input, the 3.3V may be able to control it directly (read the datasheet carefully on this point). 

You could also use a MOSFET at the input of the 5V regulator which would eliminate any shutdown current it might have, but of course the micro would have to have an independent supply. 

If your microcontroller draws less than 10mA or so you may find a linear regulator from the supply voltage a good solution- simple and reliable, though some switching regulators use special techniques to get reasonable efficiency even at very low output currents. Again, a trade-off to be made. If your micro draws uA in a sleep mode most of the time, a switching regulator is not going to be of any help, and when the 25W LEDs turn on a linear regulator won't make much difference even if the micro draws tens of mA.