I train in a cross-training dojo, and besides teaching aikido have been training extensively for over three years in Rickson Gracie Jiu-jitsu. I feel you can use aikido against a shoot almost any time. Keeping proper ma-ai is the key. When the shoot comes I tend to retreat(at a angle and not straight back) into shikko or even seiza (almost a hanmi handachi situation) I find that this is how I blend, by mirroring the attacker, and keeping my center lower than his. Just like in BJJ the person with the lower stronger base often can get the upper hand. One word of warning; if you don't have any ground fighting experience don't ever go into the attackers' guard! Sometimes it is good to remember the roots & history of aikido, namely aikibujutsu when it was a complete bujutsu.
Just my humble opinion,