Until reading the posts in response to your question, I hadn't even considered sending three ophtho letters vs. two ophtho letters and an "additional" letter. As I prepared my application, I tried to follow as closely as possible what the
SF Match Instructions said, which is, "Three (3) ORIGINAL letters of reference are required for review by the programs. No more, no less. It is recommended that residency applicants provide one letter from a core rotation." While it appears that several applicants sent three ophtho letters, I would actually propose that the majority of applicants send two ophtho letters and a non-ophtho letter from a core rotation. Perhaps a program director or other knowledgeable colleague that has gone through applications could weigh in on whether the majority of applicants send 2 versus 3 ophtho letters. At the end of the day it probably doesn't matter either way, but as I said, I hadn't even considered sending 3 ophtho letters until just now.
It may seem overly analytical and borderline OCD, but when making the decision of sending two ophtho and 1 other vs 3 ophtho letters, take a step back and assess your own application. Did you have several honors in your core rotations during your third year i.e. medicine, surgery, etc. or did you perhaps have few/no honors in these rotations. Why do I think this matters? Well, if you are going to send three ophtho letters, then hopefully your clerkship grades will speak to your strong performance in the core rotations. Otherwise, you may get questions in interviews as to why you didn't get a letter from a core rotation but instead loaded up on ophtho letters. I know it sounds ridiculous, but I can think of several interviewers by name that would have actually found pleasure harassing me during interviews if I were an applicant that had three ophtho letters AND had not performed well on clerkships. A handful of interviewers will look for a potential weakness in your application and challenge you on it just to test you. Not saying sending three is bad, but just think about it and be sure that it doesn't appear you are hiding a weakness in medicine/surgery or other core rotations. Again, while it appears that several colleagues sent three ophtho letters and found this approach to be quite successful, I would personally err on the side of being conservative and just following the instructions in the SF Match Instructions as I cited previously.
The challenge of coordinating the ophtho application and the ERAS application is the timeline. You will want to have your ophtho letters (2 or 3, depending) and the additional letter ready in time for your ophtho application to be sent to SF Match at the beginning of August. The ERAS application, however, isn't available to programs until mid-September and you will likely use several of the same letters used in your ophtho application for the ERAS application. If you ask your non-ophtho letter writers to write two letters--one for your ophtho app and one for your ERAS internship app, there is a chance they will get the letters mixed up and send the one with the official form to SF Match and the one without the official form to ERAS (translating into extra hassle for you and for them). Personally, I tried to alleviate letter-confusion by giving each letter writer two envelopes, and in each envelope I put the official letter of recommendation request required for the ERAS application. I had called SF Match previously and they said this wouldn't be a problem and they would just toss the ERAS letter of request form. I then let my letter writers decide whether they were writing to my strengths as a potential ophtho resident or as a potential intern. I don't think it really changed the content of the letter either way. Both signed/sealed envelopes were then sent to my Dean's office - the ophtho letter was put to the side awaiting the arrival of the other letters and the ERAS letter was uploaded into the system. I feel as though this approach minimized letter writer confusion and hopefully made life easier for everyone.
In summary:
1. You can apparently send 3 ophtho letters, though 2 and 1 is the official recommendation from the SF Match.
2. It probably doesn't matter whether you ask your letter writers to write separate letters for your ophtho application and your internship application. I recommend making life easier for them and just asking them to write it for your ophtho application. Otherwise, you run the risk of the ophtho letter going to ERAS and the internship letter going to SF Match (badness).