The ערוך לנר (Succah 21a) offers an answer explaining why there were so many in the second בית המקדש. He posits that פרה אדומה are very rare, it is very hard to find an animal that meets all the criteria. Therefore he says that whenever they did find one they used it even if they did not need the ashes. In other words, the reason why there were 7 פרה אדומה during the time of the second בית המקדש is that 7 suitable animals were found. If more animals had been found there would have been more, if less animals had been found there would have been less. The פרה אדומה were not done specifically out of need.
However, this does not explain the period from Moshe to Ezra:
1. How could 1 פרה אדומה last for 800 years?
2. Why didn't they make more פרה אדומה even if they didn't need them like they did in the second בית המקדש? It is logical to assume that פרה אדומה were as rare in that period as they were in the period of the second בית המקדש and therefore whenever they discovered a suitable animal they should have used it.