From what i know, there are 4 categories:
1. Loot gotten from monsters/bosses
2. Quest reward
3. Materials gotten from tools (including cane)
4. Harvested materials

1. This category is hardcoded
2. This category is hardcoded
3. This is dependant on your alchemy level, tool tier (whether standalone tool or combined tool), and location of the resource
4. They are dependant on the quality and effect of your seeds planted (quality ranging from 50%-100% of planted seed's quality)

Edit: to answer your question on quality affecting gathering tools; no, the quality of your gathering tool has no influence of any kind over resources you gather.

Well I know quality level of seeds is very important so that's good.

I also noticed that material from gathering tools had higher level based on location so getting a Plant Essence from Holy Tower area would be higher level than Pixie Forest. What I didn't know was that Alchemy Level matters and standalone tool VS combined tool mattered.

So if that is true about those two I didn't know then hey, I learned something.

I'm also well aware that Mirage Loupe has huge impact on gathered materials.

You didn't mention quality level of the gathering tools/combined tools mattering (100 quality vs 999) so I guess it has no impact. Which is honestly a good thing to me.

Sorry, just edited that part in!

The quality of the tool only matters when you combine them in synthesis as they will have a higher elemental value and you need less of them when you make or rebuild the combined tools to get the specific bonus to gathering rates.

A note on monster materials: rare drops (! drops) typically have higher quality then usual and can drop higher traits then usual.

Originally posted by Tiasmoon:

A note on monster materials: rare drops (! drops) typically have higher quality then usual and can drop higher traits then usual.

Rare drops never came to my mind, thanks for the info!

Also, are there any ways to increase rare drop rate? (Especially from regular mob kills)

Not that I know of.

I don't know if it was deluxe edition design for the house or not but one of the designs increases slightly rare drop chances.

Should be regular edition, as I had those too. Forgot they existed.

One of the styles for the Hideout says it increases rare drop chance...I assume that means monster rare drops.

I used that until I started investing in seeds and thus swapped to the Hideout style that boosts seed growth rate.

Also, what's kinda funny is that as I was making a Godspeed Boots I ended up needing a 1 elemental level Snake Slough to maximize the amount of rebuilding I could do. Well, my alchy level was near 99 at the time and even with my Mirage Loupe taken off and going waaaay back to Kurken Island, I was having a hell of a time trying to get a low enough quality Snake Slough that came with only 1 elemental level!

Beware!

Seed growth rate is kind of pointless since you can just rest for more days. All growth rate does is make them grow in fewer days. Its the stat on seeds you can skip entirely for easier crafting (untill you get duplication at which point it doesnt matter anymore)

For Godspeed Boots I didnt have that problem at all. Only problem I recall is it was hard to max its quality. Ofcourse it does also give far less stats then the Quartz Necklace(?) so its not really a great item unless you use a lot of skills.

I found there were a bit too few accessories around this time.

Originally posted by JellySG:

Also, are there any ways to increase rare drop rate? (Especially from regular mob kills)

Higher difficulties have higher drop rates.

Originally posted by Jelly:

Also, are there any ways to increase rare drop rate? (Especially from regular mob kills)

Mirage Loupe (and Loupe Compass) get effects for that, iirc.