There should be no issues with warranty as long as you stay within the proven/reasonable coding options
For example the automatic folding of mirrors is fine , but it's something you may not want to explicitly point out to the dealer as BMW back in 2010 did actually "disable" the automatic folding of mirrors to reduce warranty claims for mirror motors
. Now one can argue you still have the button and can fold them in every time you park/stop but logic does not always prevail
If your car every needs to be reflashed / updated you'll loose your customization and have to re-apply
them. Hence backup is a good thing . There shouldn't be a need to revert to factory setting before
you bring in the car. The exception being that if you changed your VO to add an option it might be safer to revert just to avoid any hassle for an upgrade failing half way through. It should not matter (as the update process will read your cars VO and not compare it to the original one (today) .
Most of the changes you can make via e-sys coding dealers can not even access via their BMW equipment. However they are logged in the system , but they are not exposed/visible to the dealer (likely BMW HW does not have access to the logging info either as it stored by the local OS on the local hard disk).