Does boiling a salsa or BBQ sauce for 30 min alter the taste?
Not really. 

Cooking something for 30 more minutes after cooking it for 30 minutes isn't going to change the flavors much more than they already had. After 30 minutes at a given temperature, most of the chemical reactions that are going to occur in your food will have occurred already. The one caveat to this is if the original cooking temperature is much lower than the second-cook. (i.e. heating it up to only 150F for the initial cook, vs. 212F for the second cook) If you're talking about boiling it for 10 hours, then YES, there will be some changes. 

Boiling the whole jar with the food inside (and the lid just barely unscrewed) will allow the whole setup to be sanitized, and thus keep the whole works food-safe for much longer than just dumping in hot food.