This whole conversation is weird. He needs stamina and the ability to output at V02 max for a considerably longer period of time than he is capable of, as a first priority. He has more speed than credited for for 1 or 2 runs and then he is completely shot and has no more capacity for anything like his initial burst and run, then he looks like he's running in treacle. His stamina and conditioning are extremely poor, but those gains cannot and will not be made until the summer, when he should be going on an arduous journey to improve his running in all aspects, from sprinting to long distance.Yep, you'd think this would be exceedingly obvious.
The other obvious point being overlooked is that whatever training Mainoo could do... all players can carry out and are clearly incentivised to do so. So even if he could somehow miraculously improve his speed by 20%, that doesn't mean he would become faster relative to the elite professional athletes against whom he is competing.
To your bolded. That would only be relevant if all footballers were put through the same training program, but if you're already a good or great runner (relative to football), you're not going to be spending the vast majority of preseason working on improving something you don't need to over whatever happens to be the weaknesses in either your body or your game - many players will be working on aspects of their strength, for example. Upper body, core or their strength related to explosiveness. The fact Kobbie is deficient with his running in all aspects means he is simply working to meet the PL bar, so yes, he can work towards that without the gap between he and them/it widening because most won't be working intensively on keeping the gap equidistant.
Kobbie needs to get some serious work in on improving his stamina; in that aspect, he is like an aged player close to retirement more than he is a youngster with his best years ahead of him, and that needs to be addressed at the first opportunity.