Will my Thai E-visa application be rejected if I entered Thailand with a visa exemption?

The user has applied for a Thai E-visa for a non-immigrant business category from Malaysia but is experiencing a pending document check. They have already entered Thailand with a visa exemption and are concerned about the potential rejection of their E-visa application. One comment suggests that if the authorities require proof of location or an interview at the embassy, the application could be rejected; otherwise, the user may be fine.