With respect, what you are describing is not how Magic Seeds works in this pack, at this time. As you have pointed out, you can not just buy the seed you want, it is random. Then you need to get enough of the needed seed to get a decent volume of essence. That means you need a very substantial number of shinies. Then you actually have to farm it, then craft it.
And that is the point I am trying to make, that it is pretty time consuming to set up a metal farm using seeds in this pack. Sure, once I have sunk a ton of time and effort in to getting all the seeds and have built it up, it will be powerful like you describe, but it is a big investment. In my opinion, quarries are a much easier option and one that many players would take. I bring that up as feedback for the mod pack maker, as I am assuming that they want people to use the mod pack more than just the regular FTB mechanics. But that is an assumption and this might be working exactly how it should.
It could be that the metals are not what Caigan cares about. Perhaps it is the exotic items, like the wither skull, that are of interest and by making it a big job to get to them, it rewards the effort. I am ok with that, end game systems should be powerful and "out of control." However, I think that the metal gathering systems of the quarry and the seeds will be mid game goals for many players and that the cost will be directly compared. My opinion (which is worth exactly as much as most internet opinions) is that the metal seeds should be cheaper than they are to make the choice more balanced. But since the entire magic seeds mod is leaving the pack, the details of pricing will need to be reworked, depending on how the new mod shapes up.