1) in different raw files i noticed differently arranged statistics:
-does way i arrange these lines have any effect on the game? for example, if i put biome and frequency right after the plant name and alcohol template at the very end with it not work?
Order of tokens generally doesn't matter, unless you try something nonsensical where the tags explicitly rely on each other.
Use basic logic - you'll have to declare [USE_MATERIAL_TEMPLATE:STRUCTURAL:STRUCTURAL_PLANT_TEMPLATE] before you can use it in [BASIC_MAT:LOCAL_PLANT_MAT:STRUCTURAL], for example.
2) which lines need to be grouped together:
-like how alcohol and seed 'use_material_template' get those sublines for value state_name and edible tags, are there other lines that need to be grouped together in the same way like biome for instance if i have more than one do i put every new biome entry in a new line or do i just put them in a single one?
Things that require subtokens like [GROWTH:xxx]. Other that that, generally no, but similar tags should be kept close together for easy readability.
-in the vanilla game's raws (from the newest 4x.xx version) after [GROWDUR:500] there is a [VALUE:X] added right after, value of what? structural_plant value is the value of the plant that grows and is picked by dwarfs, plant_alcohol value is the value of the drink made from the plant, etc but all these [VALUE:X] are added to something, this one just sits after growduration so i dont really get it.
From the wiki: "Has no known effect. Previously set the value of the harvested plant."
Always refer to the wiki before asking what a tag does. It is arguably the most important resource for all modders.
-also is it possible to make a plant grow both underground and on surface if i add both biome tags or will something take priority there? i'd like to make bloated tubers and muck roots be growable underground as well (for reasons). if i put glacier as a biome the plant obviously wont grow because it cant grow on ice but if i add underground to it, will the plant grow only underground in glaciers?
Yes, multiple biome tags do apply.
Just go into vanilla plant raws, CTRL+F 'biome', and eventually you will come across an entry that shows more than one biome tag. Case in point: cucumbers.
-i noticed that in vanilla raws strawberries are the (apparently) only berries that have a fruit template added to them so when dwarfs harvest them we get strawberries and strawberry plants, what's up with that?
Wiki page on strawberries talks about this. Yeah, it's weird.
-one last thing (for now) if i make a plant that can be milled and i put its powder material to be, lets say, iron (so you can smelt it for iron obviously) will that cause any problems? or would i just make it use normal plant material for milled form and remove its edible tags and add a reaction to the smeltery for it?
For the first, iron powder is definitely possible, just the question of whether 'Melt item' accepts it as a reagent. Second will work fine.