Using the website editor and easy make my loot tables but probably the website is outdated because have trashcan loot crate which is no longer available in rust but at the same time vehicle parts box is missing. Is there any way to add this vehicle components box and replace all parts with medium quality (2) instead of broken low tier (1) if edit the raw data file. Plugin should support it?

This answer doesn't solve the problem of junk parts spawning in containers, but the Car Spawn Settings plugin can fulfill a similar purpose of providing better parts by spawning cars with the parts in them, using a configurable random chance for each part quality and part condition.

Use of the external site is unsupported by me.
As for your question, to remove trash items either remove them from the tables or add more items to the table.
As for your other question, add the prefab to the watched prefabs in your config and reload, make sure to have the plugin unloaded and the data is deleted beforehand.

Sorry if explained bad. I wanna just turn vehicle parts crate from useless and not used by anyone into something good. I know there's plugin to spawn parts directly in cars but with better loot can just make drop better parts like I do change other loot containers with this plugin. What should I add into watched config as prefab name and if unload plugin+delete data can I restore after that because all my settings/loot drops are in LootTable file.

Find the prefab location using prefab sniffer and then put the prefab in the watched prefabs portion of the config.
You can backup your changes and then merge the two if you're so inclined, I'm just making sure it all works correctly. If youd like to not delete the data files, you can, I just can assure you it will work then.

Open oxide/data/BetterLoot/LootTables.json

find and replace carburetor1 with carburetor3, crankshaft1 with crankshaft3, piston1 with piston3, sparkplug1 with sparkplug3, and valve1 with valve3.
Save and then reload BetterLoot