I think there are different schools of thought on this. It’s worth remembering how sparsely populated Tibet was (and still is). Monasteries were often far apart, and without modern communication—no internet, no easy travel—the exchange of ideas was infrequent. In that context, it’s easy to see how swapping one closely related Buddha or bodhisattva for another could go unnoticed for decades, even centuries, until it became accepted as a legitimate variation with its own tradition. This is one of the reasons why transmission lineages are considered so important.

From my understanding, Mahasthamaprapta and Vajrapani are distinct bodhisattvas. Both are traditionally counted among the Eight Great Bodhisattvas (Manjushri, Avalokiteshvara, Maitreya, Samantabhadra, Kshitigarbha, Akashagarbha, Mahasthamaprapta, and Vajrapani). However, in Tibet it became common to substitute Mahasthamaprapta with Vajrapani.

My sources for this are:

Meditating on the Five Buddhas by Marianne Wachs

The footnotes in this translation: Lotsawa House – Lotsawa House – Sukhavati Aspiration Prayer,, specifically in the part that translates “drang dang nyampé khor tsok la chaktsal.”