I don’t think this is necessarily the problem behind what you’re complaining about. Auto-gathering is fine as long as it’s offset by a high enough setup cost. It becomes an issue with the badly designed factory houses of civs like Inca and Japan. You need to build houses anyways so making them an auto-gathering buildings essentially gives resource generation for no cost that can be set up extremely quickly.
There are other issues that make people sit in their base without consequence. Japan’s cherry orchards mean they never have to leave. And lots of people just send crates to get by until age 3 and then spam shipments and ignore map control. Maybe reducing the quantity of second crates could reduce that.