The Indomitus Boxset is a limited, well very limited boxset that might take some work at this point to get a hold of. However, it appears that a 9th Edition Starter Set is still coming. Not only that but the miniatures in the Indomitus Boxset are not exclusive and will be coming in future releases.
Personally I think this is common sense that we will see a smaller version of Indomitus as a starter set coming. It will not include the exclusive rulebook and may hopefully have a smaller rule booklet inside.
Right now there are quite a few really pissed off people on the availability of the Indomitus Boxset. There could be a plethora of unknowns as to the reasoning of what happened, but I have some insight to what happened from someone that knows.
Here is the relevant part of a communication this morning.
Regarding the Indomitus Boxset
"the rule book is the only exclusive in the box, all models from Indomitus will be available in the new starter or easy to build kits."
"local stores bought up most of the supply to resell on eBay. That is why they cut the amount they could order"