A Word about Ranges...
Yep. All nice and detailed.
However, your ranges are ... impractical. At best.
Here's somethig to consider: jump-drive based communications travel at 5 ly range increment and have a 50 ly range. 5 ly/hour is roughly 40000 x lightspeed. Or roughly 1750x the fastest FTL drive listed in the book.
If you limit yourself to lightspeed comms, with the ranges you've given...
1x10^7 miles is roughly one light minute (a little less). Which would be crossed in a little over 2 seconds by a ship using gravitic redirecting drive. And a full 58 seconds before the detection is reported. It that case, a starship will be shot at before it knows it has company.
If you assume drive-based sensors with the same ranges, the target has roughly 2 seconds (the unknown's transit time) to decide what to do. That's just enough time to make a surprise roll before entering combat. (1 minute/40000 is practically instantaneous for these purposes).
Either situation denies the use of the tactics your post is trying to support.
However, if you assume drive-based sensors (PL7 and higher), most of the post can still be used, it's just that everything within a solar system will be in the first range increment.
Moreover, I've done a bit more reading since then.
It's already covered by the rules. What you're aiming for is Jam Transmissions (the ships native emanations being the transmission in question) or Scramble/Unscramble Transmission (when you're trying to alter your sensor signature). (D20 Future, pg. 10, Computer Use skill)
Certainly, it'd be worth having a feat that gives boni to this...
Sensor Operation
Prerequisite: Computer Use 2 ranks
Benefit: When operating a starships' sensors to perform any sensor action, you receive a +4 bonus.
Tac-Witch
Prerequisite: Sensor Operation
Benefit: When trying to Jam, Scramble, or Unscramble Transmissions, you receive a +4 competency bonus.
Now, on to the rest of the post....
Proximity alarms:
Pointless. In the few situations they could be legitimate, such as combat and jump drive exits, the ship won't be able to do anything to correct things. Any other occurences would represent a wilfull neglect of duty (a criminal action).
Transponders:
Your Knowledge(Civics) checks are too high. In the modern world, this is something that occurs both frequently and easily. A compent professional lawyer (someone with at least 5 ranks and a few boni) should be able to handle this easily. I'd use a DC of 15. Note that disabling your transponder wouldn't prevent the ship from being detected, but be a signal equivalent to "I'm a non-combatant, I surrender, please don't hurt me." Seeing this in a peaceful situation probably would get you boarded, for many reasons.
Sensor Conditions:
Gas Giant, Solar, Hard Radiation: -5
Gas Clouds, Debris Fields: -2.
BTW, most of these are covered in d20 Future, pg. 10.
Beating Sensors:
These are great conditional modifiers. <yoink>
Running Silent:
The range restrictions make this rather meaningless. The ability would only be useful in combat, and the passive range works out to be 10 squares, well within many weapon ranges.