That approach may have worked in that particular case but this is definitely NOT what you should do. I am not sure how much experience you have with real bassists and drummers and live plazing? And have you ever heard about the term “playing in the pocket”?
Really good rhythm section will, depending on the song and genre, play so that attack of the bass and kick are separated in time by very specific amount. This will also help when mixing, much less need for side-chaining compression on bass. It is a difference that is very small but helps the feel of the song and help both kick and bass guitar in the mix. What you have discovered is that it is not possible to just line up all instruments when editing and get good results in a lot of cases. For instance, as I was mixing mostly hard rock and metal, more often than not, bass guitar is ideally just a small amount behind the kick. In that way they work together, first comes the click of the kick drum, than just behind that attack of the bass guitar. In that way bass guitar note acts like a sort of a body for kick drum hit. But again, some songs or even parts will work much better if bass is pushing forward slightly. So there is no formula that works every time.
When editing bass that was not well recorded (because if it was, there would be no need to edit and it would feel great, right?) it’s probably good idea to avoid using hit points and use slip edit technique, you can for instance find a lot about it in some old threads in Andy Sneap forum. Short version, cut everything jut a little in front of every note, move audio inside the clip but to not move the clip itself, cross fade everything. Use your eyes to see where the attack of the bass note is, try first with 10-20 ms behind the drum hit and when you get the feel what works best in that specific song, do the rest. Other song will ask different separation s the relationship between kick and bass note is song dependent.
Again, do it visually, you don’t need hit points, just use transients.
Your approach will get you unnutural result that may work in some cases but you are essentially cutting away part of the bass note that helps bass be defined and heard in the song. Also, whole idea, at least when it comes to natural sound for bass and kick NOT to sound at the completely same time. It also makes getting good sounding kick harder.
One more thing - when recording bass player that is at least decent, it is good idea to get from him at least one good take on one part of the song. Then you can open this good take and see where the bass notes are in relationship to the kick. In most cases that relationship will work for the rest of the song and you can imitate it while editing. Also, good idea is to finish editing drum take first, it will save you a lot of work later. If you record a bass player and then edit drum take that is not great, you will end up with useless bass take where literary every note has to be moved.
P.S. Same for the distorted guitars. On modern releases, they are often edited, quantized and melodyned. They also have their pocket, when rifing, kick will sound while pick is ending scraping the strings towards the full chord, and body of the chord will come together with the bass or milliseconds later. But it is whole another story.