Yes, that is the end! We meant for there to be a win/lose after capturing all blobs or being captured. We were down to the last minute of the jam and weren't able to quite get it to work. In the next version of the game we hope to take the player to new levels with different configurations and more/less enemies after capturing all of the blobs.
As for point gain rates, I understand how it can feel arbitrary, that needs some work. The blobs spawn with a random variance in their radius. Your point gain over time is determined by the overall amount of radius you controller rather than the number of blobs. That is the number displayed in the upper left of the screen. Your enemies probably got a lucky spawn with some high-radius blobs that gave them more money.
Thank you very much for your feedback!