A magus with Hermetic Rune Magic must develop both the Magic Theory ability and the Rune Magic ability, the former to reaserch non rune spells, the latter to research rune spells?
I'm not sure, the phrasing is indeed somewhat ambiguous.
On the one hand, the mechanics for Hermetic Rune Magic explicitly reference the ability, but at the same time, it wouldn't be possible to integrate Rune Magic into Bonisagus' theory if magi weren't truly impossible to replicate the effects with MT to achieve Breakthrough points...
I believe it takes two breakthroughs. The first to integrate Rune Magic into Hermetic Magic, the second to integrate Rune Magic ability into Magic Theory ability.
Not exactly the same thing, but in the Canaanite Magic section (Ancient Magic):
"If the magus has managed to learn the Supernatural Ability Canaanite Necromancy and is producing Insight Lab Texts by himself, then he receives no bonus for “assisting” himself, but he may choose whether to use either his Magic Theory or his Canaanite Necromancy Ability Score to calculate his Lab Total."
Maybe the same thing is to be applied to Rune Magic (so a magus researching new rune spells can use the Magic Theory ability or the Rune Magic ability).
The Major Virtue Hermetic Rune Magic (from AM p.139ff) allows a character to incorporate D: Rune and T: Inscription into otherwise Hermetic spells. Inventing such spells should be done with Magic Theory, not with Rune Magic in the Lab Total: these spells are - besides their D: and/or T: - Hermetic. Such a character uses the Rune Magic ability mainly to write, decipher or obscure runes when casting these spells.
If for some - troupe fiat? - reason the character with Hermetic Rune Magic is able to research and cast HMRE p.120ff Vitkir rune spells, your troupe also needs to decide why this is so, and how he researches them.
I think you are right about this. Reading House of Hermes - True Lineages, we can use the Major Breakthrough rules to Hermetic Rune Magic: The first research give access to virtue Hermetic Rune Magic and the Supernatural Ability: Rune Magic (converts all Breakthrough points into XP in the new ability, Ancient Magic), you don't suffers any penalty to increase Rune Magic ability. To another magus learn Hermetic Rune Magic, your must use the Initiation Rules (The Mysteries).
The second research integrates Hermetic Rune Magic completely to Magic Theory, eliminates the necessity of Rune Magic ability and Hermetic Rune Magic virtue, any magus can use Hermetic Rune Magic, just need a season of study to incorporate this advancements in your knowledge (House of Hermes - True Lineages).
Only need make a second research if you want make Hermetic Rune Magic universal to the Order.
Rune Magic is an Arcane Ability, not a Supernatural one in 5th. Ancient Magic calls it out as an equivalent to Magic Theory and Hedge Magic Revised Edition says that nonGifted can learn it without a special virtue. It would still take another breakthrough, (Major, if I had to guess), to integrate the Rune Magic Ability into the Magic Theory Ability.
Eliminating and fully integrating the Hermetic Rune Magic virtue into hermetic theory (thereby making it standard to all magi) would require a third breakthrough. Sorry shadowninja, you'll still need Rune Magic ability if you want to hide, obscure, minimize or get bonuses from the quality of your inscription. Unless you make the Dex + (appropriate Craft) roll to disguise the runes instead. [pg 140, Ancient Magic]
Research is hard.