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String-through affects the tone more than sustain. Top-loading is supposed to give a slightly brighter more janglier tone, whereas standard rear-loading has a bit more in the mids. But you can change the tone far more by changing the saddle material.
Good to know as I am unsure when the ferrules will arrive so may have to stick with top loading if I finish before then.
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Looking at the amount of thread remaining on intonation screw of the B & E saddle, you may have been able to move the bridge ahead enough to avoid that clash with the routing. That said, I don't know where your scale length mark fell in relation to that saddle position, but better to have more adjustment than you need than not enough.
I think you are right on that one, I had it so the saddle was about half way and got it pretty bang on to scale length but could have moved it back and adjusted the saddle. Thought it would be better to keep it pretty even either way in case I did get it wrong haha