Thanks again for the reply. Also, apologies for not mentioning that I did watch the AddOhms video you recommended. I had also watched ep.10 about transistors which is what prompted my additional question in the last post.
My take away from the vids were that they both can be used for switches and MOSFET would be more efficient due to no current waste at the gate. I'd also need to be selective about which one to use as I'd need the appropriate logic level type for my design.
I understood that using a BJT solution would be 'OK' when switching low level currents and I thought that might be appropriate for the HT16K33 LED matrix element of this plan. As it's <40mA (at maximum - not expected to be anywhere near that) wouldn't that be appropriate for a BJT solution?
From my reading, I'd put the HT16K33 module on the emitter side as that module would still be fine after the voltage drop from 5V to run fine. But I'd need to check/test that the drop wasn't too much.
Nevermind the above - more reading tells me I need min 4.5V for the LED controller and I'm stupid thinking otherwise. So, if I go with a BJT, the load would on collector side with a resistor between pin and base.
Would that setup be fine for a small load? From your response, it sounds like I missed a lot in the video explanation, but I did look into the suggestion of a 2N7000 MOSFET. That looks to work too and would be just as easy to use.
FYI: I'm not set on BJT, I was just thinking about the 'why not BJT' part... I'll probably just use the suggested 2N7000 based on your recommendation alone. I'll still check the datasheets so that it's applicable for my design, but I think I need to do some additional browsing on the 'why' part of that choice. There seems to be a lot of articles on BJT vs MOSFET decision which makes the choice all the more cloudy to understand.
For switching on/off the a4988 stepper module, I learnt that it might be easier to use the built in MOSFET via the Sleep pin available to cut the 12v line to the steppers and put the module into low power mode rather than using an external MOSFET for power control.
I recently found this helpful page so as to learn through failure and several of the cases (especially #3) include those you mentioned. 
For testing all at once - heck no. :o I'll be checking each item on it's own, writing code that works so I understand that component as well as possible on it's own. I'll refactor that code and then add individual systems one at a time to ensure it all works together. eg: Throttle control first with stepper, then (in rough order) numeric displays; indicator light arrays; buttons and switch array; instruments using servos; instruments using steppers.
By making it modular and keeping track of the current draw vs my power source, I hope that will keep things managed. Initial post was to ensure I get my head around things to consider regarding powering of the project with difference voltages. I've read ATX PSU might also be an option down the track.
I fully expect that I'll need a higher speed Arduino than my current Uno for the final build due to speed / memory. But for just learning each of the components, the Uno should be fine I think. At the end of the build, I might even utilise that Uno as a subsystem to just manage LED lights and non time sensitive indicator outputs. (I can live with a 1/2 second delay for the gear indicator for example.)
Sorry - more wall of text:
My experience so far (specifically to this build - I've played around with utilities monitoring with battery powered sensors):
HT16K33 - running 2 quad 7segment displays and custom code. Used to learn multiplexing, modified the adafruit library to generate 8 digit numbers and learnt the wiring required for both chips and LEDs. It's underpowered (datasheet says 4.5-5.5v) at the moment at 3.3v and draws 14mA with all '8's across all 8 digits (no dot points), so it'll draw the expected 20mA (on max brightness) once I move it to a 5V supply and <10mA on the lowest brightness (which would be the ideal level).
Note: I know it's not the most appropriate chip for driving quad 7 segments displays (no internal alphabet, etc...), but it was on hand and it forced me to learn a few things at once just to get it to work. I'm plan to tear it all down and use the knowledge about the array for the individual LED indicator lights in the cockpit.
MAX7219 - still being delivered, but from my messing about with the HT16K33, I feel better about the possibility of playing with these, the 7segment displays and writing code for it once they arrive. I also think it'll be better to power them in groups of 4 in series to ensure sufficient power.
MCP23017 - No experience on the IO extenders as yet as I'm waiting on a $2 pack of 100 crap buttons. Was only going to use the buttons and other parts just as a practical learning exercise about building and coding for a button matrix. There lots I need to pick up here with button de-bouncing, handling rotary encoders, rotary switches, 3 stage toggles and the coding needed to handle each. Not relevant to this power chat though. I'll put up a separate post if I get stuck, but there is a lot of reference material out there already.
Steppers & Servos - I'm hesitant with these due to the required higher external voltage and all the things to cater for in the reference link I mentioned so as to protect the Arduino pins. This hesitation is also what prompted me to avoid powering anything through the Arduino at all so I would learn more about power control in circuit design. I plan to use the Arduino for logic control and build/utilise the required circuits to disable power to the systems when required.