Fortunately, we have an advantage that R’ Yosef Engel did not. In the early 1950’s the Maharal’s Chiddushei Agados was discovered (most of it, at least – some masechtos are still missing) and printed. Now we can see what the Maharal himself had to say on that gemara. Here’s a link. The Maharal takes as a given that a neshoma needs a container. The few cells that are there at conception cannot possibly hold a neshoma. What is there at conception, says the Maharal, is the “koach” of the future neshoma.
In other words, according to Maharal the gemara does not conclude, as the simply reading would indicate, and as R’ Yosef Engel understood, that the neshoma enters the body at conception. What the gemara means is that since the potential for the neshoma to enter the guf at day 40 exists at the moment of conception, that potential is enough to sustain the guf until the neshoma actually arrives.
Based on this reading, Rashi is beautifully meduyak. Rebbi heard Antoninus’ argument and “m’devarav lamaditi,” concluded on his own, not that the neshoma is there at conception as Antoninus held, but rather that the koach of the future impact of the neshoma is sufficient to sustain the guf.
Just as the future entrance of the neshoma 40 days later already has an effect on the guf from the moment of conception, the impact of Yom Kippur 40 days hence already impacts on our lives now, from Rosh Chodesh Elul, creating a climate of eis ratzon.