The Control Settings allow for up to 4-button combinations per action and the code behind the control settings section seems to take button sequence into consideration. For example, there is no conflict between CTL+Z+X and CTL+X+Z, see below pic.
Unfortunately, the code that calls/triggers those functions/actions seems only to evaluate the buttons collectively. So both actions for CTL+Z+X and CTL+X+Z are performed at the same time in the sim.
Can we have the sim’s actions take button sequence into consideration?
@katIX3647: Don’t forget to vote for your own topic! 
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Don’t ctrl, shift and alt offer enough combinations without any risk of conflicts?
I can’t understand why you’d use the style in your example. I’m surprised the sim even allows it.
One reason (for me, at least) is that it is easier to remember that S+R is for “Set Run” than SHIFT+R, when one has so many other SHIFT / CTRL / ALT+Something combinations. Then again, maybe it’s just age catching up with me… 
While the example is perhaps silly to some extent, I think it’s possible for some real cases to come into effect over time - the point is that the user would not realise it.
For example, I tried to map Shift-V to toggle the Visual Assistance option (markers etc.). That clashed with Photo Mode, so I used Ctrl-Shift-V instead.
Fast forward some weeks and I might end up wanting to mapping something else to those keys, related to ‘V’. If I’ve forgotten that I’ve already mapped them and use the same buttons but in a different sequence, it seems it won’t warn me. So it’s a relevant point to catch such cases. Good find
If you bind the same combination to more than one axis it will tell you, via the ‘1’ shown here…
Assuming the conflicts aren’t conveniently next to each other, clicking the gear icon on the right of each assignment will show you what’s conflicting and even has a button to go directly to it…
I appreciate that is the case, but in the original post, no conflict is shown yet the same keys are used, just in a different sequence. Looks to be an oversight on the development side if the sequence in which you press the keys is important, not just which keys are combined.
I haven’t tried it out myself, so if I’m misunderstood the OP then I apologise
No, you’ve understood correctly. It seems as if the dev group who designed the Controls UI took button sequence into consideration, but that design was never realized for whatever reason (time constraint?) by the other group(s).
The way things presently are, there could be unseen conflicts. So remove the potential conflicts by giving us more options.
You’re not alone 
Engine
Reverse Thrust CTL+E+R
Cowl Flaps CTL+E+C
Oil Shutters CTL+E+O
Manifold Heat CTL+E+M
Afterburners CTL+E+B
War Power CTL+E+W
Lights
Lights (all) CTL+L+1
Cabin CTL+L+C
Flashlight CTL+L+F
Beacon CTL+L+B
Landing CTL+L+A
Nav CTL+L+N
Taxi CTL+L+T
AP CTL+A+1
Flight Director CTL+A+D
Altitude Hold CTL+A+E
Level CTL+A+R
Heading CTL+A+H
Localizer CTL+A+O
Nav CTL+A+N
Approach CTL+A+P
Increase Heading Bug CTL+A+]
Decrease Heading Bug CTL+A+[
Increase Target Alt CTL+A+HOME
Decrease Target Alt CTL+A+END
Set VS CTL+A+V
Increase VS Rate CTL+A+PGUP
Decrease VS Rate CTL+A+PGDN
Set FLC CTL+A+F
Increase Airspeed CTL+A+UP
Decrease Airspeed CTL+A+DOWN
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Wow, that’s quite a list - and not the easiest combinations to use, often needing both hands! But there is some nice logic to them
I try to keep any custom key bindings as simple as possible, often by removing some default key bindings which I won’t use anyway.
Example being custom views. I don’t mind using Ctrl/Alt etc. to save custom views, but to load them I just want a single key for speed and convenience. So I use Numpad 0-9. I just have to remove other default bindings that might clash.
Side note:
Does MSFS 2020/2024 still support the ‘delayed’ key press logic? One of the old MS sims used to let you open specific doors by pressing a two-key combination (Shift + a letter), then, within a second, press a separate key on its own (1, 2, 3 etc.) to choose which door to open. I can’t remember if it was pre-FSX or FSX itself that did that. I have no need for it; just came to mind as it was quite unusual, and the new sims sometimes have legacy features left in 
