Some blocks use item textures which are separate from the 3D render of the block they represent. However, a large amount of items still lazily use the raw block texture instead. This makes it unneccessarily difficult to texture the block and item differently as new model files need to be created, and in some cases is actually somewhat of a parity issue as Bedrock Edition has unique item textures for some of these blocks.
The fix is simple: just create duplicates of the block textures and place these in the item folders, and make the item models refer to these files instead. Further tweaking could be done to make their item textures more item-like, and possibly center them better for better visibility in the hand. Alternatively, these items could be made to have 3D item models that more closely match their block form.
Blocks which correctly use unique item textures:
Lantern
Soul Lantern
Campfire
Soul Campfire
Chain
Bell
Redstone Repeater
Redstone Comparator
Cake
Cauldron
Hopper
Flower Pot
Nether Sprouts
Sea Pickle
Kelp
Seagrass
Bamboo
Sugar Cane
Oak Door
Birch Door
Spruce Door
Jungle Door
Acacia Door
Dark Oak Door
Crimson Door
Warped Door
Iron Door
Oak Sign
Birch Sign
Spruce Sign
Jungle Sign
Acacia Sign
Dark Oak Sign
Crimson Sign
Warped Sign
Blocks which should be converted to have unique item textures:
Oak Sapling
Birch Sapling
Spruce Sapling
Jungle Sapling
Acacia Sapling
Dark Oak Sapling
Crimson Fungus
Warped Fungus
Brown Mushroom
Red Mushroom
Dandelion
Poppy
Allium
Azure Bluet
Blue Orchid
Oxeye Daisy
White Tulip
Pink Tulip
Red Tulip
Orange Tulip
Cornflower
Lily of the Valley
Wither Rose
Rose Bush
Lilac
Peony
Sunflower
Crimson Roots
Warped Roots
Weeping Vines
Twisting Vines
Dead Bush
Cobweb
Torch
Redstone Torch
Soul Torch
Lever
Tripwire Hook
Glass Pane (+ variants)
Iron Bars
Ladder
Rail
Powered Rail
Detector Rail
Activator Rail
Blocks which should be converted to have unique item textures due to parity reasons (these use a constant tint, which is completely unneccessary for an item, as the image file itself can just be directly colored instead - this is how Bedrock Edition does it currently):
Grass
Fern
Tall Grass
Large Fern
Vines
Lily Pad
Attachments
Comments

Why would they create a model system that allows for reuse of textures when appropriate, and then make redundant textures anyway? This is obviously intended

why is the lily pad not in the center of the chest hotbar

@unknown That has nothing to do with this report. Though you can report it as a bug if one doesn't exist already.

Do note, that for all the ones that use separate texture files as item forms, they actually look different than the textures used as block form; only chains don't fit in that category. Lanterns need a different file or the chain part would be part of the item model (or it's need to create a custom model file, rather than builtin/item), seagrass needs to not be animated, and nether sprouts were moved up for visibility, the block model isn't unique, and wasn't made unique just for that change.
Can confirm in 20w48a, although in my opinion, this is most likely intentional.

Sounds like a feature request
Can confirm in 20w51a.
Can confirm in 21w03a.

Saplings are intentional.
Can confirm in 21w05b.

Affects 1.17 Pre-release 3