ChemDraw Beta 21.0 Portal
When adding bonds to chains and cyclohexanes, bad bond angles are drawn and or unexpected behaviors results when the "point" of the stucture is down. You can see the results in the MainChain.jpeg where the red arrows point to the poorly draw bonds with the very bad bond angles. I drew this by hovering over the atom on the chain or ring and pressing 1 or 0. Note!: 0 gave long bonds and not in the opposite direction of the green dot–weird. Cleaning up the structures (in this case) fixed the poorly drawn bonds. I know that I could press 9 to sprout the 2 bonds at once, but that is not something I have routinely used.
Using Solid Bond tool first bond is created at 30 degrees angle. Increasing of the chain adds next bond keeping 120 degrees C-C-C angle. A position of the bond being added to a secondary C-atom is placed further away from 2 neighbouring C-C bonds: all 3 C-C bonds at tertiary C-atom are at 120 degrees. Extra bond at tertiary C-atom is placed at 12 o'clock. If it's occupied, then 30 degrees clockwise. That's why 4th bond at the "Y" shaped tertiary C-atom is added at 12 o'clock, but at the "Mercedes 3-star logo" shaped tertiary C-atom - at 2 o'clock [for a second scenario I would prefer it to be at 6 o'clock]. In any way, I would consider it a matter of preference. As you stated, it's easily rectified by applying "Clean Up Structure" command or "pressing 9 to sprout the 2 bonds at once" during drawing step. That "green dot–weird" gives a clue where the bond will be placed as well.
Alternatively, you can draw a bond in any direction:
Using a bond tool, click and drag from an existing atom or an empty area in the document window. The bond is drawn in the direction you drag the cursor.