Depends what you’re targeting with those overrides really.
Generally yes Easy Tune will apply overrides that sit comfortably alongside existing SCOM tuning. There’s no need to remove overrides to get Easy Tune to work.
Using your disk tuning example, if my memory serves me, the default Server tuning packs don’t meddle with disk tuning (it’s pretty organization specific). So these should sit comfortably alongside your tuning.
However if there is overlap with your existing tuning and a Tuning pack the standard SCOM order of application still rules. So depending on the conditions you may find Easy Tune wins in some cases and the existing tuning wins in others. If you are worried about it you could just use the enforced flag on your existing tuning rather than letting it come down to some of the woollier tie breakers such as depth from root node. Easy Tune will flag up if it finds other overrides against the same workflow on the same target, so you would be able to see if there is some sort of conflict (non-managed overrides is how it flags them). But this is done after tuning is applied.
The Enterprise version does have some additional mitigations for this, and you can pull existing tuning into a tuning pack to re-apply with Easy Tune.
Additionally the tuning packs are just CSVs under the covers as you’ve seen, so if there are any workflows you definitely want to steer clear of, you can just select those rows and delete them from the tuning pack, or add in your own level and re-apply them!