This is of great concern to me as well.
Training methods may vary, but at the core they must be working the same things because they are developing very specific qualities and skills. Thus, if more than one system is producing people with the same skills and same scope and complement of skills, the differences in developmental training are superficial ones.
What Takeda did for personal training is likely lost to the mists of time, secrecy and lack of recorded records; the presence of aiki in members of succeeding generations is proof that it was successfully transmitted by Takeda's teaching; the presence of aiki in the descendants of those students indicates that whatever means they devised to teach aiki skills, was effective.
Sagawa revealed some of his training methods only late in life, but those with whom he shared it have aiki. Horikawa likewise was able to transmit aiki to selected students, as there are descendants of his training today who have aiki and are teaching it. They are also recognizing that the training methods other systems outside the Japanese internal martial arts have the same critical components, and likely pre-date anything that Takeda and his aiki descendants possessed.
Rather than worry about things, it is more productive to note that if one has IP and aiki, whatever means that was used to develop it was effective. But even more important, before one makes these pronouncements, one should actually go out and experience IP and aiki so everyone is on the same page regarding what is being discussed here.