Your clarification is my intention. Still...If I'm cleared to taxi to a runway...I'm cleared to cross everything enroute to that runway...unless restrictions are given by ATC. Active/non-active are not terms used in this matter.
You are correct. 'Taxi to Rwy .....' gives you the right to cross any and all runways/taxiways EXCEPT the Runway you are instructed to taxi to. Active, inactive, taxiways, all fair game.
I don't know why a controller would tell someone to hold short of the runway they're assigned. That does two bad things. Forces you to have to say 'holding short,' and also could get you in the habit of NOT holding short since you weren't told to previously. This may seem silly to some of the more experienced drivers here, but to someone with less time under their belt, it might not seem that out of reason.