Hello
1- 5496x1960 in 1x3 isn't real "5496x1960" it's actually 1832x1960 de-squeezeed to 5496x1960 to get a correct aspect ratio (that's how 1x3 mode works).
You should compare 1832x654 3x3 vs 1832x1960 (5496x1960 after correction) 1x3, now you would notice the more details in 1x3 mode (in addition to no aliasing, less moire).
1x3 mode is the sweet spot between 1:1 and 3x3, if you want the absolute sharpness you need to use 1:1 modes, cropping 1x3 footage in post isn't a good idea, it's more like cropping 1080p footage.
2- Upscale it directly from MLVApp --> in Export settings --> resize. You need to take care of aspect ratio, if you have exactly 2560x1440 MLV and you want to upscale it to UHD, set 3840x2160 in "resize" settings, But if you have for example 2560x1280 footage, and you want to upscale it to UHD, putting 3840x2160 in "resize" would result in correct width, but the height would be stretched from 1280 to fit 2160 resolution (Taller aspect ratio which isn't correct)
You need to calculate the AR manually 2560x1280 upscaled to UHD would be 3840x1920. Not sure why MLVApp doesn't calculate AR automatically, it isn't implemented.
3- Provide a picture how LiveView look like, give a short Sample MLV (you can shorten it in MLVApp from "Cut in & Cut out" tab, 2 frames is enough).