The Materials from every Mod that registeres it's Items at RegistryEvent.Register not being available(without forcing the Material).

Any specifics? I've never had an issue with this.

For Example:
if i am using Cucumber, Mystical Agriculture and TriGems it wont load Ruby, Topaz and Sapphire(The Gems from TriGems are in the OreDictionary and they are used by Mystical Agriculture if i am forcing the Materials).

The oredictionary checks for some of those crops are basically useless unfortunately. If the mod doesn't load and register its ores before MA then they wont work. This is the main reason I added the ability to force enable crops.

I tested that out with my own Mod before reporting.
If the other Mod registeres its Items at RegistryEvent.Register (to the Forge Registry and the Ore Dict!) (its recommended to register the Items there.) Mystical Agriculture doesn't knows about them.
With registering the Items on preInit it works.(without changing anything else.)

As far as I know there's no reliable way to make this work for every mod. I have to add a check myself to see if each mod is loaded. I'm going to be taking a different approach in 1.13 for this which should hopefully fix problems like this.

For a prime example of this, if you load thew Mod Embers rekindled, the base Mod Ores of Copper, Tin, Lead, Silver wont show seeds unless you force them, which i suspect is a matter of how it either registers//loads as you've indicated.

I think you can load all your Item registration and OreDict Checks on RegistryEvent.Register with prioriry LOW to fix this.
But i tried to change/Fix that in your Mod(before reporting because i wanted to open this as pull request) and i were not able to do that.

That would not work for ALL Mods, but i think for the most of them.

Github allows to remote close Issues with Pull Request for other Repos?