Basically like enhancements WOULD stack, BUT the amont of tiers still available to purchase would reduce on all trees when you purchased it from one. Tooltips would state which enhancements are 'overlapping' or 'count as the same enhancement'.
So basically you would puchase "Str Bonus: Class Based" from the Kensai tree which has a tooltip saying 0/3 before purchase and 1/3 after purchase. You would then look at the SD tree and see "Str Bonus: Class Based" which had a 0/3 listed would now list 0/2. The points spent on that enhancement would count towards the kensai tree since you bought it from that tree. Later you might buy the next step from the SD tree.
The assumption here is that tiers will have flat progressions based upon the indications given by the develops, but if some retain an increasing cost then the tiers purchased later would cost more points and count towards more points on the appropriate tree they are purchased from...
For example, let's say that str bonus costs 2/4/6 AP based upon the tier purchased. You would then have two points spent in the kensai tree for the first tier you purchased and if you bought the second tier from the SD tree you would have 4 points purchased in that tree.
As for Kensai Weapon attack bonus and a proposed assasin knife attack bonus...let them stack. Really specific weapon choice bonuses will presumably be limited in application to one specific PrE tree or be part of the kensai tree. That is unlike something like 'str bonus' which would presumably be in alot of PrE trees.