I think the reason the average assistant's gathering rate is over 90% is because they're mainly looking for materials that are accessible to them, what's high in demand that they can handle to retrieve within their own power, the common varieties, if you will. Materials of different grades and ranks will of course be different in rarities and where they can be found, as well as the success rate in gathering them and bringing them back in good enough condition to be used for alchemy.
Ruby, on the other hand, has been unreasonable and driving Lloyd up the wall demanding the highest quality/ranked materials that can be found in areas you'd likely get killed in. Like, I get the stress of fulfilling expectations getting to her, but did she even take a look at how dangerous getting some of those high-quality ingredients can be? Forget about being able to get them, she should be lucky Lloyd had been coming back alive. Lloyd's gathering rate may be 40%, but if we look at how likely people can get the materials he's been forced to gather, especially the rarest and highest quality ones, 40% would actually be an astounding achievement when the success rate is typically 5%, as an example. And putting himself into dangerous situations on a daily basis, pushing his body and mind to the brink of collapse, it would make sense that his magic would be strong enough to produce such results. His capability in magic could be on the level of court magicians, maybe even a 'royal' magician or sage, thanks to all the hard work Ruby forced on him. A blessing in disguise, if you will.
And once Ruby finds out how much danger she's been putting him through, if she truly cares for Lloyd like she displayed during that flashback, she's going on the guilt trip that topples any other and realize how fucked her relationship with him has now become, if it's even still there. I'm getting the popcorn for when that time comes.