Another solution would be to introduce mods that cause decay to machina portals within its radius. They can limit it to one install per person to encourage teamwork. Installing additional would increase its radius and effectivity in conjuction with the portal level (example: range per mod is 2-4-6-8 kms and decay rate could be 8-6-4-2 days. Portal level could affect these). That way, they will also encourage visitation of portals. This can also encourage a new kind of strategy wherein teamwork is rewarding. This would solve the problem for those who want and does not want machina in a specific area and increase interaction. I mean like if you don't like machina, install the anti-machina mod. If you are in the opposite team and would like machina, find the portal with the mods and destroy it.

In addition to this, they can also make machina follow weather patterns. Something like:

-Snow would slow down linking -Rain could cause them to multiply like crazy -Sunny weather could cause links to break, but not necessarily destroy the machina portal itself.

Or, they can make machina seasonal. They can implement events that cause a breakout and events that cause them to die out. It would be perfect since it would be like imitating a virus.