Monster Melo said:

What exactly are the penalties for boosting stronghold any time that's not cvc?

There aren't penalties, exactly, but there are a few drawbacks that could as well be labeled penalties. Let me share some strategy-relevant info... 

 As TURBOMASTER mentioned, your stronghold is a big source of points in the CvC, so that is when you'd want to boost. Often, the points earned from completing stronghold processes during CvC might make up half your clan's points or more. Each upgrade or transformation that finishes outside of CvC is one less that could earn your clan its next CvC victory or checkpoint. 

Boosting the stronghold can be very expensive so you want to make sure you're doing it at the most optimum time. The expense isn't just in the cost of boosts, it's in the hundreds of millions of resources required to make a timely transformation. You don't want to use up your boosts and resources completing transformations before CvC and then have to scramble to build up your stock with hours of sending slow march after slow march while you should be actually competing in the event. Outside of CvC, it's best to just fill up your storage and let your stronghold processes take their time. 

Last note.. Completing equipment drafts doesn't give points and most drafts take a LONG time. So, it's best not to bother boosting those at all until you have members ready with all the materials & ingredient gear necessary to craft whatever is being studied. 

Monster Melo said:

 I hate seeing our chief so stressed out about this.   

well, it was the case with our chief...

now, it is solved... anyone who boost transformation/construction/research in the stronghold outside cvc is quick off the clan... same thing during cvc if it is not asked to do it...

we was plagued with this problem for weeks... have take a long time but observation of who is online ( when unwanted boost have happen ) have allow us to find the guilty and ban him from our clan...

we was plagued with this problem for weeks... have take a long time but observation of who is online ( when unwanted boost have happen ) have allow us to find the guilty and ban him from our clan...

By the way, being chief mean to be stressed out... you have not time to play, so much busy with diplomacy and trying to solve million of little problem... have be there but now i am happy that i am not chief or elder anymore... i can finaly enjoy playing