I believe aikijujutsu may also rely more on offbalancing to perform the technique which may also require or include atemi. Jujutsu depending on the style may focus less lon the offbalancing aspect prior to performing the lock or throw. Aikido on the other hand generally speaking doenst prefer to use atemi (strikes) they generally prefer to use the oppenents initial momentum.
Withaikijujutsu, aikido, and jujutsu alll being variations of the same stuff joint locks and throws, from my limited experience i would say aikijujutsu is in practice the middle ground between aikido and jujutsu although the parent art.
In other words aikido focusing more on the off balancing and "softer" aspects, plus some reliigious stuff blended in, and jujutsu depending on the school going the other way, but there is still alot of overlap, and probably mainly variation in how particular locks, throws and techniques are executed.