dont try to make things more difficult. If a place asks for 3, send 3, not 2,not 4. we dont look at extra letters.
i always viewed the whole application process like this :places get WAYYYY more applications than spots and need to "trim down" these numbers when considering who to interview. Some things are out of your control (like what level they set their USMLE screener at) and others (like following their particular application requirements) are easy to follow tto keep yourself from getting weeded out for some dumb reason like you only sent 2 letters and they want 3. All those silly supplemental applications and requests for your college (and sometimes high school) transcripts are, in my opinion, easy ways for places to cut down to the people who are not just adding their program to their list to "apply to enough places".
good luck, its a frustrating process