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.
Either from ripping your own Blu-rays to MKV, or downloading an MKV, you have a very large video file that needs to be standardized by encoding to MP4, which is more accessible for devices. (And smaller in file size.) A Blu-ray player will play a data DVD or data Blu-ray with either MP4s or MKVs on it, and your computer will play both MP4s and MKVs, but you might need to stick with MP4 on other formats, such as with phones or tablets. Most importantly, you need to encode to MP4 to save space.
The best software for Windows (at least my version, which is Win 7) is XMedia Recode, which is freeware. I first get an MKV that’s significantly larger than the resulting MP4 will be. (The MP4s I make — and I recommend this setting — use 2,000 kilobits per second bitrate, which works out to about one gigabyte of size per hour of video. So a two-hour movie will encode down to a two gig MP4, and I would choose an MKV original of at least four gig size.)
The dimensions of the video (such as 1920×1080, 1280×720, and 854×480) don’t matter in relation to the eventual file size of the MP4. Just the bitrate. I think of the bitrate as representing the amount of detail packed into the video. One side effect of this being true is that you need to consider the appropriate bitrate for various dimensions. You could make a 1920×1080 video with a bitrate of 2,000 kbps, but it’s going to look the same — and be the same file size — at 854×480. I think of 2M as being appropriate for 480p, 4M as being appropriate for 720p, and 8M as being appropriate for 1080p. You can do whatever you want, but for a video to be a “true” 1080 — in a relative sense — it should have a bitrate that reflects its dimensions.