1) 'We use accent marks written over vowels' - you also underline stressed vowels, but didn't mention it
2) 'if we talk about the "Default Stress", we're talking about stressing the 2nd-to-the-last syllable; and in that case, the accent mark is usually omitted / not written' - I don't doubt that this is true, but in the dictionary you underline stressed vowels even if they are 2nd-to-the-last syllable
3) 'This accent mark is known as a pahilís and is a slanted accent mark that leans up and to the right. It is written above vowels, and indicates that the syllable under the mark should be stressed.' I've seen many underlines in dictionary words without the pahilís
The way I interpret your system is the word is stressed on the underlined vowel, and any of the 3 accent marks above a vowel indicates a glottal stop