Earlier quoted context omitted.
From the pricing docs you qouted - the smallest standard instance is an F1 which costs $0.05/hr and has a 600mhz cpu + 128mb ram. Compare this too flex VMs where the smallest machine is $0.038/hr and have beefier CPU and 3.75Gb of ram. Doesn't it always make sense to use the flex VMs? The only downside being min 1 instance and slower autoscaling.
waprin's comments are on the nose with what we've experienced. There are pain points with the flexible environment that we don't have to worry about at all with standard runtimes. The two biggest ones for us are slower deployments and a lack of monitoring tools. Just today we actually switched one of our App Engine modules to Flexible runtimes out of necessity as we we're hitting quotas for App Engine infrastructure,…
Most of these have gotten a lot better since managed vm's first rolled out (3 years ago!?!?!?!?!)