There is no easy answer. It depends on the facts related to what is being changed on the aircraft and how it relates to certification requirements and the impact on the safe operation of the aircraft. That's the difficulty with discussions on aircraft modifications.
There are no one size fits all rules. It depends on what you are doing. Too many people approach these problems like, well this worked for that one, we must do that for this one. NO, that does not work!
You go back to certification requirements and major vs minor questions for what is being changed. Also everyone's privileges are different depending on what operating certificates and rules they work under.
I've seen vendors accuse the airline I worked for of violating the FARs because the rules the vendor (and STC holder) was certified to operated under were more restrictive than the rules the 121 airline operated under in certain areas.
In that case a Part 21 parts manufacturer and STC holder could not just make a minor alteration to an STC (because it's FAA approved data). But we could make FAA minor changes to wiring on an airplane (where and how connections are made) because we were an aircraft operator.
The devil is in the details. Certification and installation requirements for any two modifications can be worlds apart depending on what system is being modified and how it impacts aircraft performance and operation.
Exactly. How often does the airplane we are modifying exactly match the STC? Say the STC was initially installed on serial # 93 all the STC drawings are based on that airplane and we are modifying serial #375. Often times wiring and connectors on the STC prints doesn't even exist. If the connectors do exist, we may not be able to use the pin locations specified on the STC prints. This happens time and again with bulkhead feed-thrus.
Maybe STC says to install the box somewhere such as an avionics shelf in the baggage ceiling, but there is no available space.
What deviations can be called minor vs major? It gets muddy and why there is often more than one person making the call what data needs to be acquired and approved.
TCAS STC's come to mind. They are getting pretty muddy when one TCAS upgrade has multiple issues. Its a simple box swap for newer software right?
#1 Airplane manufacture SB, but the SB isn't approval to install it. Instead it says something like "These changes are approved under STC xxxx and is chargeable to the owner/operator"
#2 There is an AD against the TCAS and it says to modify it per the TCAS manufacturer SB #A1, but the TCAS manufacturer doesn't do A1 anymore. Instead they modify beyond that to a part number in the STC.
#3 The TCAS STC itself has a letter in it saying it is an AMOC for the AD and contains a pile of limitations in the AMOC letter.
You can't really make assumptions about anything. Everything is case by case. Without all applicable data to review, how can an informed decision be made?