Where the percentages add up to 100 that seems to make sense. 500 iron (96% steel, 4% steel scrap) gave me 94 steel and 4 scrap, which is close enough given that this is probably subject to the RNG. But 2000 copper, 1000 iron and 1000 gears (94% gun turrents, 60% scrap) gave me 96 turrets and 20 scrap - the 96 I can see, but how does 60% result in only 20 scrap?

Sounds like you might be on v.0.0.12, because the percentage thing changed in v.0.1.0. Anyway, here's how it worked in 0.0.12 (the percentages are probabilities):

For each gun turret cycle, there was a 94% probability of creating a turret, and a 6% probability of creating 10 military-scrap. So, for 100 cycles, you should get an average of 94 turrets, and 6 (x10) military scrap ... AVERAGE. It sounds like, in your example, you only got 2 (x10) military scrap, due to the randomness, as you pointed out. The probabilities are multiplied by the # of pieces, so 6 (x10) should give you 60 for every 100 cycles; instead you only got 20.

As of v.0.1.0, the 94% probability was removed, and the 6% remained. For 100 cycles there, you should get exactly 100 turrets, and, again, an average of 6 (x10) military scrap. But wait, there's more! In v.0.1.2, I introduced mod settings, where you can control the probability of each scrap type.

I'm currently working on updating/balancing recipes for the next version (and other changes), hopefully coming out soon.

I hope I answered your question successfully. It's those probabilities that can lead to head-scratching moments. :)