After testing this issue out, I can finally draw my conclusions
I took to purple runes (Yellows are bit precious), and I took the artisanship up to lvl 6, then moved it to one side, then I took the hawkishness and put it up to lvl 4.
I had the lvl 6 artisanship on the left side and the lvl 4 hawkishness on the right side, and clicked 'specifically' the combine all, now they were the ONLY two runes on the rune board.
The lvl 6 artisanship went into the lvl 4 hawkishness, make it a lvl 6 hawkishness.
I tried the same thing with a lvl 6 tranquility and a lvl 4 tactics and the exact same thing happened...
Then I took the lvl 6 Hawkishness from earlier and dragged it on top of a lvl 3 partisan, only this time the hawkishness absorbed the lvl 3 partisan and because of the hawkishness current exp it stayed hawkishness and lvl 6, but gained the exp from the lvl 3 partisan.
Then I took a lvl 6 tactics and lvl 4 mesa, instead, this time I had a stash of runes to go with it.
The lvl 6 tactics was on the RHS and the lvl 4 mesa was on the LHS, and I had a stash of only green runes.
Still the lvl 4 mesa absorbed the lvl 6 tactics with everything along with it.
Next, I took a lvl 3 cunning and had it on the LHS with a lvl 6 mesa on the RHS, along with a stash of green only runes.
I hit the 'combine all' button and this time the lvl 3 cunning went into the lvl 6 mesa along with the stash of green runes on the RHS of the lvl 6 mesa .. the lvl 6 mesa became a lvl 7 mesa.
So, what I conclude is that if you have 'specifically' have the SAME TYPE OF RUNE and NO MATTER what the same type of runes are on the LHS and the RHS of the rune board, the rune on the LHS WILL combine with the SAME CLASS OF RUNE on the RHS