A few things:
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Good job on the fixture! You may want to use a shorter bolt for the back left corner to avoid accidental collisions with the a tool going to or coming from the tool height sensor. You might also want to consider using L, C or U channel for your next iteration, as that won’t flex like flat stock does, so it’ll clamp the stock with even pressure across the surface. The flat bar will flex, so it ends up pinching down on the corners and bowing over the middle.
As long as you can keep from cutting into it, that should work like
a champ. In fact I may have to make myself a pair of hold-down bars myself!
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Does your y-axis have any play at all in it when the machine is on? When it’s off the motors won’t resist you, but when it’s on you shouldn’t be able to wiggle anything without using a fair bit of force. It’ll only move once you’re exerting more force than the holding torque rating of the motor. If you have any wiggle, refer to this thread about how to fix it, as that’ll resolve any backlash that could be causing the unevenness in branch size a poor cut quality.
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The grain in a given wood makes a huge difference how things will come out—wood with larger grain is much more likely to splinter & not hold small features well, especially if your cutters aren’t really fresh and sharp. It looks (at least from what I can tell in the pics) like you’re using red oak—you may want to try something with a finer grain to see if you get a better result in it.
Looking forward to the next cut!