FIL would consistently call MIL by her first name to DH. I didn't get why this bothered me until just a few years ago -- he died in 2000 -- when we were sifting through our own midlife first family issues. In some cases the usage could be just a casual warmth, but FIL was a terrified, self-absorbed, emotionally violent man. Calling his son's mother by her first name to his own son struck me as a possessive claim on ALL her focus, identified her to their own child as specifically not-Mom. What bothered me is that it was done as part of overlooking the child. In the OP's case it feels like part of an obvious connection with the child.
You know what's worse? Having your father call your mom "your mother" like it is a dirty word. THAT is nasty. Having a man call his wife by her name is NOT nasty, and it's not a subconscious way of diminishing her motherhood. Calling a spouse by the parenting honorific, IMO, is weird to me.
OP, I don't speak in the 3rd person to anyone (hearing it is like nails on a chalkboard to me) and hubby (having grown up in a household where his parents called each other daddy and mother and found it weird beyond belief and pretty gross as well) used my name, so DS never even realized I had a title. Well, he did call me "Milk" for a bit, since he would ask for milk and I would respond. :) DH told him that he was "papa" so DH got called that...but I never used any of the titles for myself with him. Just didn't see the point. So he knew my name is Molly. Which, frankly, is so close to "mommy" that most of the kids of my friends got it mixed up anyway, and I was tired of it by the time I had my own kidlet.
A few months ago, though, and he's 7.5 now, he started on a kick of using the title. More than one. So I'm now getting mom, mama, mommy (cannot stand that one), and ma (b/c I said I'd rather hear "ma" than "mommy"). It's odd! I blame it on his acupuncturist, who tweaked when she heard him call me Molly, and was stern with him. I didn't think he'd take it seriously, but he did. I'm am thoroughly annoyed with her (I was mainly annoyed with her before) as it was NOT her place to do it.
Lastly....supposedly I called my dad by name once. I don't remember this. I guess he was very clear in the concept that I am not to call him by name. I called my mom by name. It did start in anger, at 4, when she divorced my dad (for many good reasons, which I was sadly very aware of), but it just ended up being who she was. She was Judy, and she was my mom. And I respected her 1 billion times more than I respect my dad, no matter what someone else might think b/c of the name/title I used for them.
I'm just surprised that your SIL didn't know this about you guys! My MIL hates it, but she deals with it, since she's heard it lots of times. (she just about fell over on their last visit, when DS referred to me as "mom")