Yes your phone will still be working with a deodexed rom. If that particular deodexed rom develops rotational issues when deleting system apps (an issue I've never come across when it comes to deodexed) Then choose another deodexed MM rom. It may be that the deodexed with the Magisk root method incorporated as part of the rom (su binaries) is has better network connectivity (wifi, Bluetooth, 4G LTE). That might be the case being that back then, Magisk was the new kid on the block. I wouldn't attribute a better data conection to Magisk but to the rom itself. This doesn't mean you can't replace Magisk with Chain Fires SuperSu. It only means you have to know how to go about it.
If my priorities were to run banking apps, Netflix, pokemon and had no intressed in Viper4Android, Double Atmos, Xposed firmware, full R/W access or a permissive overclocked custom kernel and needed to pass Safty Net checks with ease then Magisk would be my choice. Both methods have advantages over the other.
One rom I flash had Magisk in-corporated with the rom. I then flashed SuperSu .zip on top of Magisk. Well 2 separate su binary rcause issues galore, sometimes subtle and then begin to increase over time. My inital thought wete that flashing SuperSu would replace Magisk. It did not. I rember wanting that rom for some particular reason and so I used a root file manger to look threw the rom. I then removed the Magisk files,folders snd I think it came with busybox applets that also needed to be deleted. Its been a while, I think I might have examined a seprate Magisk.zip in order to determine what had to be deleted from the pre rooted magisk rom.
PS:
https://root-checker-pro-free.en.aptoide.com/app
Download the app above, Its the only one I know that shows the path and status. If it looks like mine its good. If it shower Multiple busy boxes installed correctly let me know.
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Oh: I had to flip kill back botton setting back to on in an exposed module. I rebooted turned it off and rebooted and left side bar work again.
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