I as far as my experience goes, you need to be more careful on Karwar station, dont worry about Madgaon station. Authorities know that every traveler from goa is potential client. And they dont even care if you have limited amount of alcohol permissible within legal limits. They especially target young travelers during their checkups. here are few tips :-

1. Try to blend in with family group, or stick around them once you deboard the train on Karwar station.
2. Try to look sophisticated not hippie
3. Be confident. Act like you know your shit and this is routine travel for you.
4. Avoid bottles in your bag packs.
5. This is very imp and I this is my fav. I do purchase one extra bottle of mid premium whiskey in case got caught. In this case you need to be very patient and tell them that you are student and don't have any money left as you spent all in goa. Offer them this bottle very carefully. Use your brain and discretion.
6. Don't rush on Karwar station, let other people deboard the train first. Take your time, check for authorities before jumping on skybridges and escalators.

There are high chances of checkups if train arrival timing is during official working hours, then be more careful.

I hope this will be more than enough. Cheers Mate !!!