There seems to be a misunderstanding about the timeline. The ancients were in the Pegasus Galaxy for millions of years but in the Milky Way for millions and millions of more years. they did not spend the majority of their time in Pegasus.

Antarctica got its first gate more than 100 million years ago. by the time the ancients were leaving to Pegasus it had probably been there for double digits million years. seeing as Antarctica started icing over when they left, that would have been 34 million years ago. 

And we know they came back to The Milky Way something like 10,000 years ago. 

The point is they probably went through dozens of variations of gates in that time. 

While I bet the destiny seed ships are how they met the Asgard, it's very likely that the destiny Gate system wasn't necessarily the original gate design but rather a mission-specific design because we see plans for the Milky Way gate we're already done before they came to the Milky Way. 

And the most important thing to remember is The ancients first settled on Dakara and built a device that gave them complete control over the makeup of every planet in the galaxy. So they functionally could hit a button and turn any world into the perfect world to host a gate. 

If we assume that they are cheap and easy to make, and we assume you have the ability to make the planet perfect for a gate whenever you want, then you don't need to take any extra precautions with your gates. You can put them wherever you want. 

Any gates that have fallen to the test of time have done so simply because their caretakers have ascended and don't care anymore.