Hello Seth,
Thank you for your reply about your Chronomatic. The 3 -6- 9 minute markings are from the old days of telephone timing in Switzerland as mentioned before. They have no application in military or aviation. I served in the Swiss Army and also flew a large variety of airplanes over a 30 year span (including Airline Operations) and there was never an application or need for a 3-6-9 minute reminder.
Keep in mind that the Swiss watch makers/ designers think primarily of Swiss use. Vary few think about the use outside of Switzerland.
Heuer, Breitling and a few others started with the Hour bezels in the sixties because Pilots requested that feature so they could have "Local" time at their destination without having to reset their Watches. (Travel through different time zones). These are generally known as Tool Watches. I have used a Heuer Autavia GMT for 25 Years.
As I explained in a previous Posting about BEZELS, there are many applications. My personal opinion is that a minute bezel on a chronograph is redundant since minute time-ing is more accurately done with the chrono function. So an hour bezel is much more useful.
Back to minute markings , one can see 5 minute markings, usually in colored segments and those are for SAILING to time the start of the race.
Your watch is certainly interesting with the red dot at the 3 minute mark and I must assume the dial designer wanted to give the user a reminder for their phone cal. As mentioned, was common back in the 40's and 50's and later became superfluous and was no longer seen on watch dials.
Reference for the Telephone call markings are explained in the BOOK by Gerd-R Lang and Reinhard Meis titeled "Chronograph Wristwatches To Stop Time" Dial Indications page 25. It is an excellent reference for Chronos. Enjoy and let me know if I can help further. Heinz.