Re: bokken vs bokken?
Yes this is pretty standard practice in many aikido dojo.
What you are describing is Awase work.
This practice develops blending or timing. This is the harmony of aikido. As uke cuts tori evades (tenkan) then replies (irimi)
Move too soon...and uke will not cut where you were but will follow you and cut where you are.
Move too late...bang!
So you look to move at the instance that uke attacks. In his attack there is an opening for you to seize.
As has been mentioned ...the larger moves associated with weapons are easier to see and understand.
Also the increase in distance between uke and Tori means that an understanding of the influence of 'Maai' - distance can be incorporated into practice.
In essence this paired weapons work should be identical to unarmed tai jutsu. This makes it ai ki do.
If there are special moves just for weapons then this would make it technique orientated and more of a jutsu. Not any less effective but just not aikido.
aikido weapons are aiki-ken, aiki-jo or even aiki-club! If aiki is not present it becomes for instance kenjutsu.