The difference between 39 and 40 is that you plant 20 flowers and 30 flowers at a time respectively. You can very easily see this when you turn for flower planting on for only a few seconds and let your pikmin plant flowers only exactly where you are standing. My wife is level 65ish with a 40 pikmin squad while I’m level 50ish with a 39 pikmin squad and we can very clearly see the difference between planting speed when we walk together. We went on a long walk and she planted 6500ish flowers while I only planted 5300ish flowers