I'll try to clear a few things up using my experiences in tree breeding so far.
1) To improve the mutation rate or breeding rate in general, only three factors will help. First is increasing the density of leaf blocks of the two target trees. Some trees have more leaf blocks than others naturally (e.g., Apple Oak vs. the abundant Ebony tree saplings). So if you want to say breed apple oak trees with the ebony tree, you'll probably want to plant 4 apple oaks to 1 ebony tree saplings to square out the leaf blocks on each side. The second factor to increase breeding rate is the number of bees you have in the area. I have 6 apiaries going right next to each other in a straight line. They are looped. The more bees you have looping and the more leaf blocks are available, the faster leaf blocks will be bred. From my experience, you never need more than 4x of a single tree. So at best, you'll do 4x of Tree A, and 4x of Tree B. The only exception to this rule is the Balsa which has incredibly few leaf blocks (i.e., average of 5 leaf blocks per tree). The third is the pollination trait. You want to get the maximum pollination trait to maximize tree breeding rates.
2) Alvearies do not increase breeding rate. They only increase the range of the bees for tree breeding. I consider this to be a con because it increases the chance of bees breeding leaf blocks that you may not want.
3) Based on my observations, I do not get the sense that mutation rate is "per bee cycle". Because this implies that leaf blocks are converted per bee cycle, and you clearly do not see this. I think what the % means is that when you DO get a leaf block that is successfully bred/pollinated, then you have a % chance to have it mutated. Otherwise, it'll just turn into a hybrid of tree A/tree B.
4) There are no traits that increase fruit maturation from what I can tell. The first trait, sapling, impacts the rate of you getting a sapling when the leaf block naturally vanishes/decomposes after harvesting the wood of the tree. The yield trait impacts the chance of you getting a product of the leaf block, if any (e.g., chestnut). Sappiness, from what I've seen, is related to some biogas thingy that's not related to fruit maturation. So unfortunately, this thing will simply take time. However, even my fully-modified chestnut tree, after waiting for all the blocks to fully mature, gave me 9x64 chestnuts. That is a lot of chestnuts. Just know that leaf block maturation is timer-based. So if you plant a field of chestnuts....it may lag as all the timers are keeping track of each individual leaf block until it matures.
5) Breed one tree at a time. It'll make things much easier.
6) Use a chunkloader if you're not in the area.
I won't write more about going into strategies for modifying tree traits, etc. If you have specific questions about that, I'd be glad to answer them.
Hope this helps!
