To avoid the boil over, simply move the flask to the side such that only 1/4 to 1/3 of the flask is receiving heat from the burner. Then, turn the heat down. This will allow you to create a low, rolling boil in the flask like you do in your brew kettle. Just monitor the heat so that you maintain only enough heat to keep it rolling Any more is unnecessary and will cause a boil over.
One thing to be cautious of is making a starter with pilsner malt that you intend to pitch whole. The flask, by its shape, is designed to minimize vapor loss. The vapors collect on the side of the glass and slide back down into the base liquid. Thus, you do not boil off any DMS from pilsner malts or extra light DME. If after you make your starter you are going to chill and decant the liquid, then no big deal. If I need to boil down my wort or am worried about boiling off flavors compounds out, then I will boil in a pot first, then transfer to the flask. Then I will boil in the glass for 5 minutes just to make sure everything is sanitized.
Lab grade glassware will handle any stove and can be immediately dunked into ice baths. The only concern is the depth of the ice bath. Make sure it is not much deeper than the liquid inside the flask. If you have 1-2" of wort in your flask and you dunk the flask in 6-8" of ice, then you do risk cracking the upper part of the flask that is not also in contact with liquid inside.