Boiling in a pot can work but when working with yeast you have to be extra cautious with sanitation. The reason for boiling in the flask is you eliminate the chance of infecting a batch while transferring from the pot to the flask and it ensures the flask is totally sanitary as well. If you do choose to boil in a pot inside of the pot I would recommend using a stainless steel pot rather than non-stick so that you can take a lighter to the rim of the pot where you are going to pour it into the flask.
I have made about 30 starters, Boiled in the flask for only the first couple. I rinse everything in Starsan, never flame anything, make step starters and have had no issues.
Do you guys who do not use fermcap ever have issues with krausen spilling out the top of the flask? That is another thing it is good for preventing. The one drop I add before boiling solves the boil over issue and reduces krausen.
I don't use fermcap in my starters. I use a stirplate and rarely get much more that 1/8 to 1/4 inch of krausen.
I really don't understand what the issue with fermcap is. The amount that ends up in the final beer from one drop in your starter is minimal. If you use a no rinse sanitizer small amounts of that end up in your beer. If you use bottles instead of kegs then even more sanitizer ends up in the beer. For the most part my beer is just barley, water, hops and yeast with the exception of minerals because my water is really soft and the one drop of fermcap.
Starsan is just a very weak acid and water it just changes the chemistry of the water. Fermcap is silicon. I don't really worry about the silicon and use it occasionally. It is recommended that you filter it out of the beer. Though very few do this since it settles to the bottom and stays in the trub that gets discarded.
I was curious about how much that one drop really is so I did the math. In my 10 gallon batches that one drop is close to 1 part per million and potentially even less because I crash cool my starters so I can pour off the wort and just pitch the yeast. So in a 5 gallon batch the one drop in the starter would be 2 parts per million or less. The FDA guidelines require it to be less than 10 parts per million which it already is way under. What this doesn't take into account is that yeast will also work to eliminate the fermcap, basically any that is left after fermentation has adhered to the yeast so when you move your beer from the yeast cake, the final product in the bottle or keg with far less yeast in it is going to have way way way less than the one or two parts per million you started with so with the 10ppm guideline and only having a fraction of a ppm in your final beer I think you should be good to go.
If you are really worried about it I think there are also some more natural oil based anti-foam agents.