Something like that could be implemented. Personally, I wouldn't until you start modifying a drive below its installed specification. My reasoning is that the slower drives aren't that way because the vessel they're on requires a more dependable drive, they're slow because it's cheaper (and cheapness rarely translates into "more precise").
For
modified
drives, I'd encourage the GM to
upgrade
the difficulty, probably with Force Points*, despair meaning the **** thing just broke, requiring either a lengthy fix or some quick jury rigging (which will inflict system strain).
* If you require a solution that occurs more frequently than this (justified - look at the falcon) upgrade the difficulty but add a boost - things got more random, but you're not actually punishing the guy for having a better engine.
Edited by Col. Orange