I've seen this type of situation many times. In theory, the approved data which permitted the installation of the updated equipment should include a flight manual supplement with a revised checklist, if there are any changes to operating procedures for the modified aircraft. This is not certain, as this step gets bypassed often. For every STC I issue, I consider, and state if necessary: "Install in accordance with:"[Installation instructions], "Maintain in accordance with:" [instructions for continued airworthiness (ICA)], and "Operate in accordance with:" [flight manual supplement (FMS)].

Sure, in some cases, there is no change to one or two of those (at least one will be affected, or why are you changing the aircraft?), but yes, some changes are transparent to the maintainer or pilot, so no ICA or supplement are required. In accordance with the criteria for "major modification", if one or more factors are significantly changed, an STC, or other approved data will be required, and those factors should be considered and dispositioned with a document as above.

Now we find that the very worthy legacy aircraft are attracting many mods, as owners update them, and this is great. And, these updates create mods on mods. The problem is that A mod may have a lower effect on the aircraft. A second low effect mod in installed, and now it combines with the first low effect mod, and the effect is not low any more. But neither STC suggests that it could combine with another mod to be higher effect, and certainly the original aircraft manufacturer (and certification basis) have no way of considering this. For this reason, every STC certificate includes the words:

This is really broad, and a big burden to the installer, who likely does not have the technical capability to evaluate the combined effects of multiple modifications. One of my projects for a client, has been a plane jane C 182P, which thereafter had 27 STC's incorporated during one modification period (including glass cockpit, autopilot two alternators, amphibious floats and reversing propeller). That airplane became a very different airplane to operate than left the factory. Some of the mods came with approved FMS and checklists, but again, they did not mesh well, as supplemental checklists for one item, did not consider the many others. The result was that I developed and had approved an FMS for the combination of mods, and associated checklists.

So I get that there may be a genuine need to amend a checklist to consider a new or changed system, that the 1960's manufacturer did not consider, and that may fall to the pilot/owner. Better something than nothing. And, if that amended checklist works well for the pilot/owner, that's helpful. But exercise caution, if a less familiar pilot flies the aircraft, and does not have the underlying familiarity or experience, a gap or flow discontinuity in the home made checklist could create a bigger safety deficiency. There is no one size fits all solution for this, and the more mods which go on legacy aircraft, the more complex the situation becomes. To add to the complexity, the newer private pilot, updating their newly purchased legacy aircraft may be creating a plane which even their instructor never knew, so they were never trained to handle correctly. I can assure readers that the 182 amphib with 27 STC'd mods, handed to the couple of hundred hour total experience PPL owner,
required quite a lot of additional training. I flew about 100 hours with this new pilot, who delightfully learned like a sponge. He would have had difficulty finding a flying school instructor who could have comprehensively trained him on that aircraft.

Awareness of the need for documented, disciplined procedures, which hopefully have been through a qualified evaluation for content and flow is a good idea.....