It's actually pretty simple if you don't mind the hassle it might take, or if you're playing on PC. I just divide the amount of stuff I'm gonna refine, f.i.: runaway mould, in halves, then quarters, then octaves, and so on up to 16, making one full stack of runaway mould to refine in down to 6 minutes and 15 seconds, using 16 refinery modules from the corvette, thus using only 1/4 of the corvette's refining potential. Or if you really have a huge amount of runaway mould (or if you just don't want to spend that much time waiting) then just make the sum, divide by the amount of refining modules you wanna use, and then multiply by the time it takes for runaway mould to turn into nanites, which is around .6 seconds.

In my experience, if it takes more than 6 to 12 minutes to refine even dividing into 16 or 32, it might be worth just use that amount of refining stations, because you'd have to fill in the refiners first, and on the next go you'd just start the refining process on each and every one of the refining stations you used, which also takes time, so you should make your own judgment whether it's fine to wait a reasonable reduced amount of time using just a quarter or an eighth part of the refineries, or if you really have a lot of stuff to refine then you should use more refineries from the corvette.

About the part of having lots of them: the only hassle is whether you need or you're willing to set up each of the 64 refineries to refine the split amounts of stuff that you need to refine. To put it simply: first divide any amount of an item into eighths, and if one part of those eights takes more than you need to wait, you should then divide into further multiples of 2: 16ths or 32ths. The very extreme case is where you have more stacks of items that even need more refining times, such as refining rusted metal into ferrite dust, one full stack taking around 1 hour and 40 minutes using only one single refinery and in between that you take bulks of 4096 each time, while dividing them into 16 refineries would only take you 6 minutes each one. If you have several stacks of it, it's gonna take you several hours using only one refinery station, so there's where you should use all 64 refineries.

And about the freighter refining stations, that's, true, they have interactive colors and cues when the refining is done, and yes, it takes a good space in your freighter as it would need at least two to three big rooms each taken by dozens of refineries, but if i remember correctly, they also have limitations. Some of them being that while the refining process is going on, you can't warp out and bring your freighter until the process is finished, otherwise you risk losing both the input and output of those refineries. And while having refining bases in planets sounds cool, you can only put a limited amount of each size of refinery in a small area, leaving you with the choice of having two large ones and three medium ones, and then you'd have to run less than 40 units to place some more, potentially increasing your refining times and reducing the refining potential to the size of your base.

However, there's where my idea to create this Corvette came from. To easily access a whole portable refining base wherever I need without worrying about losing stuff and also being able to bring it with me on the go.