David, your family tree is definitely complex in my mind and it sounds like you have a good handle on it.
I created a private separate tree for my son's birth family. He has no interest at this point of developing a relationship with them, but I wanted it to be there in case he does. Actually I found them by accident while on Ancestry. It was not an open adoption and it was not a private adoption, so the info should not have been there for me to find. It's a very long story, but the short version is that I came across what I thought was his original birth record and after much searching and comparing I was able to confirm my suspicions.
You and I agree that there are very likely non-blood ancestors or descendants of our ancestors that we are not aware of. In the case of those we know are not related by blood, I believe we should note it in the tree and keep going.
The fact that on our personal trees the relationships aren't accurately designated for step-grandparents just means that the system is not perfect. I guess I never expected it to be. It sure is far better than anything I could have done by hand or by a less sophisticated family tree type program.
Last night I played around with the relationship of my husband's step-dad. At this stage I am going to leave it as no relationship, but I did like that I was able to do a blend family, something not available on Ancestry.
That means that when I have my husband's step-dad on the screen the listing of children below include the two from my mother-in-law's first marriage and the one she and her 2nd husband share.
I just had to be sure I set it correctly so that it didn't somehow connect her first husband to the son from her 2nd marriage. And it didn't somehow connect her with all the children he had from his 2nd marriage.
Clear as mud?