I mean you never know. The last 3 "transformations" on super weren't called Super Saiyan 4
Because the power scale's entirely beyond the realm of GT. Normal SSJG was capable of when clashing with another God-level being, ripping apart a universe when one lacked control. I'll let that settle in: Goku was able to, at a far lower level of power than he is now in the series, with normal SSJG, able to threaten the existance of the universe when fighting Beerus because he couldn't control his ki right. His every punch is capable, should he please, of destroying the universe with a punch. The fact he hasn't mauled Caulifla, Kale, or anyone else, is because he hasn't learned to control that instability in divine techniques such as Hakai (like he did in the manga, mind you).
Also having a younger body wouldn't really affect God since it's just producing God Ki, which requires very specific control and utilizes no SSJ at all. We know God is above SSJ3 simply cause Goku favored it over SSJ3 once he got serious vs Caulifla+Kale, only showing SSJ3 as a lesson to the girls. Basically put God is possible at any time or place for Goku because controlling Ki is not the same as physical issues caused by a younger body (lessened stamina, namely. Muscle memory issues, etc).
Considering Blue is simply adding Super Saiyajin to God once you can properly control God's Ki, then Goku could STILL use Blue during GT, and it would STILL produce far better results than SSJ3. The stamina is an issue, but Goku used it for a long period of time while exhausted vs Kale and Caulifla, but could barely hold SSJ3, implying while Stamina consuming, it isn't as bad as SSJ3, meaning again, better pick to use vs Baby!
Why does all the above matter: Simply because it proves that, were DBS canon to GT, Goku would have used God or Blue instead of had his ass whupped time and time again near the hind end of the Baby Arc. Also SSJ4 never shows a fraction of the force that SSJG or SSJB have. Not only that, but 17 wouldn't suddenly obey Dead!Gero in order to fuse with Copy!17 to form Super-17. Because DBS-17 clearly loves his family - both his wife and kids and his sister and her family - that he wouldn't let Gero control him (IN FACT, it's been made clear he RESPECTS Krillin for freeing him from any vestiges of Gero's control like the bombs).
What else? How about the additional wishes on the DBS DBs which are not referenced in GT? How about why the crew didn't think of requesting the Grand Priest/Beerus/Champa to gather the Super-Dragon balls to wish the Black-Star Balls innert?There are 1000 reasons that anything that's happened in Super thus far effectively omits GT as a possible occurrence.
Edit: This is excluding points like Goku could have asked for Whis' help with the BS (Bull-Shit? Black Star? Same difference) DBs since Whis could have traveled them over the universe instantly. Shin's alive in GT, therefore so should Beerus and by proxy Whis is active. Beerus would have AIDED them to PREVENT Earth - his main culinary source - being destroyed. Or that Bura is YOUNGER than Pan, yet somehow OLDER than her in GT. Or or, how about the fact Krillin went bald again during SUPER, which isn't that far behind now, and aimed to become a warrior again to protect Marron?
Holy mother of god saying 1000 reasons might be overshooting, but simultaneously it's not.
Edit 2: Before you ask, "But Vartio, what about Ultra Instinct!?", I can ACCEPT Ultra Instinct not being there - when he's in child form - because instincts are built into your body. having your body suddenly change shape will mess with your instincts. So I'm not even including UI here, but the two that suddenly turning into a boy would have 0 effects on Goku - God, and Blue.
Edit 3: A few minor clarifications to the start. Tl;Dr: if Baby was really such a problem, he could have used Hakai on him. We know he can use it.