Confused about Vaal Crystals

Loved all the goody drops in campaign vaal mechanic that don't drop now in maps.

In campaign it was Run thru 6, go to temple, set rooms, run.

Now in maps (beaten the Archy once) I have gotten 2 medallions for extra crystals, so it's at 18.

So i run 6 maps, and get 6 crystals, but on the 7th map, the Vaal Ruins pops up, so I go and set the rooms, and then go back to 6 more maps, but when I go back to the temple, there are no more rooms to add.

So I run the temple, and it's horrid, 4 barracks, 3 commanders, 2 are level 3.

No Benches.

My Workshop level 3 had a bench, but when I went back to the Vaal Ruins The Temple Closed....

And there was 6 crystals lit up and I could add 6 more rooms and run a mew temple?

So what is the point of extra crystals; shouldn't it be RUN 18 Maps, set 18 rooms, run your temple?

Help a confused exile.

same, im so confused.i cannot store more runs, only 0 out of 6 when i click run temple every time.