> Once you have apps which use significant resources and persist non-trivial amounts of data – i.e. what most developers work on – the difference becomes a lot less significant

If you spin up the VM once and it runs for days/weeks that is true. In a cluster scheduler environment you usually have immutable images where every change requires replacement of the workload. In such scenario your VM or container might get replaced a few time a day, during every deploy. That's where VM startup time becomes an issue.