People overstay in Thailand (whether accidentally or intentionally) all the time. If they get to the airport and pay the fine there is generally no repercussions returning to Thailand.
Some reports of people who have applied for visas for other countries but denied because of an overstay stamp from Thailand but returning to Thailand is usually not an issue.
The evisa system routes your application to the embassy or consulate that serves the state you live in. You do not go to the actual embassy or consulate. It is all done online. Your visa is sent to you as a PDF attachment. You print that to show immigration on arrival.