You are correct re: breeding. If you are Min-Maxing your lineage, you should only be breeding one type of seedbed at a time, and waiting for their offspring to be born before breeding again. Min-maxing like that is also the only time where it would make sense to use feeding to boost your lineage, and it helps to offset some of the slower growth. That being said, you don't strictly need to min-max to be successful, and often times what you need is just more goblins, not necessarily better goblins; not to mention that to get the various endings you will likely also need to be breeding just to grind down sanity.
For combat it's a little more complex. The DEF of your leader actually doesn't matter until all the pack units are dead, since all damage is done to the pack units before any is done to the leader. High DEF on pack units will, however, help keep them alive. The game doesn't handle each pack unit individually, it handles them as a pack with stats that are the average of all the goblins in the pack. Higher average DEF in your pack means fewer die when you are attacked, though the game does include that if you really overdo it and have invincible goblins at least 1-3 will die every time they are attacked regardless of stats. Improving DEF to keep leader units alive if things go south is also worthwhile. I couldn't find the function to decide which goblins die, I assume the weakest. This is also why command is not really worth improving, since it doesn't actually improve the stats of your pack (it could actually reduce them, since it will bring more low-tier goblins with you).