We mostly try to adhere to the Mendix best-practices, only adding or adjusting them when we feel it's beneficial.
For example, we also use the SUB prefix in microflow as it makes sure there's always a similar order in the microflows for an entity(if you don't use SUB, the ‘sub’ microflows for an entity starting with a ‘AB’ would be on top, while the sub flows starting with ‘ZZ’ would be on the bottom of the list).
Another example is the folder structure. We usually adhere only an Entity Related folder structure. For example a flow ‘SUB_Order_SetStatus’ could be triggered by multiple processes, thus organizing them by process makes it easier to forget to reuse the same logic(an increases the changes of unwanted duplicates). For this same reason we also always organize the documents within a folder to group them by their document type(Microflows, Nanoflows, Pages etc).
Adhering to the best practices is really important in our opinion as it makes it much easier to onboard new developers to a project and helps devops to do their work better.