Always difficult to answer questions from holders of passports different to mine, or to people I've travelled with. But the e-visa should certainly work with major land borders: Chau Doc isn't a border crossing, the formalities are carried out under the authority of the Song Tien border post - the official name, if you need to put something on an application form, although (confusingly) it's also known as Vinh Xuong.

But if you have a couple of days in Phnom Penh then it's easy to get a visa through the Vietnamese embassy/consulate there. It's a well trod path, and if you throw enough money at it you can get sorted in a day. It'd probably be $10/20 or so extra to get the express service.