The idea is you can use computer programs or character skill - using skill instead of a program does not mean dumping the programs rules.
Then I see few situations (aside from having little in form of software) where the skill would be used. Let's imagine the player has Gunnery 2 (a good gunner in CT). he may use the Gunner interact and have a +2 , or he can roll as your tables, and getting as I understand your tables) a DM of 0 on a 5-, +1 on 6-7, +2 on 8-9 and +3 on 10+. Do you really he will risk to have an extra +1 on a 10+ by risking a lower DM on 7-?
The advantage is it gives players playing the game something to do during ship combat.
And while I applaud and share your intent, I'm not sure this will achieve it ,as the players rolling for it are the same ones that are involved in ship combat (except the engineers doing damage control, that will be involved but not use this rule). The ship's Doctor, to give you an example, unless he's also a gunner, will stay equally iddle unless there are casualties, and if so he will be involved regardless if you use this house rule or not.
At best the Navigator will be involved while he was not (unless he's the same person as the Pilot ,as i've often seen)
See above, to which I will add many of the PC scale ships have a model 2 computer max
Do you consider the Gazelle or thetype T Patrol Cruiser PC scale ships (I myself do)? I ask because they need at least a model 5 and 3 respectivelly for jump...
I guess we run very different games.
Probably, but I guess almost everyone finds at times a character or two uninvolved with the current situation (probably they will be the protagonists in other scenes, if the referee is worth his salt).