Do NOT run the lines through the bottom of the mast to through the arm to LNB.
1. You will have to take off the LNB in order to pull out the wires. This simple act will change the alignment enough to kill your KA signal from 103/99. I know it sounds hard to believe, but you're just going to have to trust me on this one.
2. You can't run the cabling up through the base due to extra bracing/ballast weight that the AT-9 dish has in the mast. This added metal makes it almost impossible to run all 4 lines through it. You would essentially have to remove all the connectors and thread each individual cable up through gaps between the metal brackets and the mast.
3. In order for the dish to pass a QC inspection, the bubble level included with the dish kit must be installed in order to indicate that the mast is still level after installation. As far as my region goes, it's somewhat hit or miss as to whether the installer actually does it. But if it's in there, that will also block the cables from passing through.
running the lines inside the mast will not disrupt performance. the mast can actually act as a shield against any interferance.
Interesting premise, but there's probably little truth to this statement. Any interference powerful enough to pass through the jacket, braiding, inner shielding and dielectric of the RG-6 would most likely have little problem ingressing into, through, around or off of the mast and into the cabling. In reality, most of the noise inherent in the signal traveling on coax is introduced through the LNB, leakage into connections (at splices etc.) or signal reflections at splices, wall outlets etc.