Usually (at least my Thomson and two Sony Trinitrons) TV holds two predefined set ups, one for 50 Hz range and second for 60 Hz range.
If You change something when You have started 60 Hz game (or close like 59,3 Hz or 61 Hz) for example Rygar then it affect all games in that range like Bank Panic (61 Hz) or 19xx (59,63 Hz) or even neo-geo games (59,18 Hz). The same goes to 50 Hz. Start Stone Ball, change something in service menu. It will affect also games like Raiden Project (53,98 Hz). Sadly I don't remember in which range TV puts 54,7 Hz (midway games) or Irem games (55 Hz).
I've seen somewhere (Youtube and/or here on BYOAC) user that managed to set groovymame so he have to set one parameter - vertical size. All other parameters were set using custom modelines. But in my opinion that will be very time comsuming. Depending which frequency Your game use will have to shrink or stretch vertical size. From my experience the best way is to use slope option in service menu as it only shrink/stretch picture only only from the bottom. Note that geometry will also change.
Horizontal centering is also needed many times. My TVs does even option for this not also in service menu but also in standard menu. It's needed when I switch from megadrive to amiga (both real hardware).
About that arcade_15 mode. It's ok for typical TV but for trynitrons I have it caused to loose some part of picture on the upper and lower part of screen so I decided to use custom monitor that will shrink picture a bit. Try game Rastan and see if it cut some highscore on upper part of screen.
BTW. Since You asked me about this in personal message I can skip it, right?