The 16:9 box for 480p is 854×480. An MKV with the dimensions 1920×800 (2.40:1) will fit that box with the dimensions 854×356 (using a modulus of 2).
If you have, say, an MKV with dimensions 1920×796, it’s not meant to be that way. It’s due to one of two things. Two pixels were accidentally cropped out of the original on two sides, and they’re retaining the aspect ratio by retaining that error; or the wrong modulus was used, and it’s now technically in the wrong aspect ratio.
Either way, when resizing to a 480p MP4, pretend you’re dealing with the usual dimensions. (In this case, assuming 1920×800 to convert to 854×356.) You might be fixing the aspect ratio, or slightly altering it, but it will not be visually discernible.