You've already highlighted the differences - the entity validation is always enforced, while the microflow validation is only enforced when the microflow is triggered. You could have one page form where the custom save microflow triggers the validation, and a second page form where another save button does not perform the validation. Also, you could probably avoid the validation by using the API to save a record.
Having said that, I don't think it should be an issue for you to replace the entity validations with microflow actions provided you find all the places that your record can be updated and make sure the validations are run if needed. Using right-click - find microflow actions on your entity should help finding all the places you need to decide whether or not to run the validation microflow.