Is there a difference between Skyfire and Jetfire, canonically speaking?
As I understand it, Hasbro picked up the toy rights to the Macross Valkyrie, so they called him "Jetfire", painted him white and red, said he was an Autobot, and sold him in America.
Then when they were making his cartoon/comic book tie-in, they discovered that they didn't have any animation rights to the character (because the Macross anime was a thing). So they decided to significantly redesign him.
Someone at Hasbro then said that if Jetfire was going to be so significantly redesigned, kids wouldn't make the connection, so they should change his name to "Skyfire" and worry later about making a toy for Skyfire and finding a way to include Jetfire in the cartoon. Skyfire's name wasn't an accident or an animation error.
The comic books got the memo on the redesign, but they didn't get the memo on the name change.
Since the plans to grow Jetfire/Skyfire into two seperate characters never grew to fruition, he remains one character, who sometimes looks different due to licensing issues, and at some other times he's referred to by another name.
Amusingly, since Hasbro lost the toy rights to the Macross Valkyrie and they're never getting them back, the redesign turned out to be a blessing and the character can still have toys made of him, and since he has toys "Skyfire" has actually fulfilled the conditions for becoming his own character, independent from Jetfire, but his name has become commonly accepted as Jetfire, with Skyfire being his less often used alias.
Not any more or less than between versions of the same character in comics and cartoon, which is to say, quite a lot. For example (and from memory, so I could be wrong), in the cartoon the Dinobots were created by Wheeljack in modern times after being inspired by a dinosaur exhibit, while in the comic they were created back in the age of dinosaurs by the Ark, and lay dormant until today. Jet/Skyfire is the exact opposite; in the cartoons he was an old friend of Starscream that crashed on Earth and lay dormant in ice millions of years ago (before the war, even), while in the comics he was created by the Decepticons in contemporary times and telekinetically disassembled / turned to Autobot by Buster (long story). Interestingly, this makes Jet/Skyfire a Decepticon turned Autobot in both continuities (for completely different reasons), decades before Drift made it popular.
Although it should be mentioned, in the cartoon Skyfire was a fish out of water with no knowledge of the Autobot/Decepticon conflict. He trusted the word of his old friend who had to
actively lie to him about both the Autobots and the Decepticons (and get others to play along) in order to make him chose Decepticon. When Skyfire realized the truth he rejected the Decepticons and joined the Autobots.
In the comics, Jetfire was a mindless drone, programmed to obey Shockwave, until his control was wrestled away by Buster (still just a puppet). Solidly under Autobot control, Optimus Prime gave him a personality, and Jetfire chose Autobot, but previously Shockwave seemed confident that if
he had been able to give Jetfire a personality, Jetfire would have been a Decepticon (which kind of casts a shadow on Jetfire's "choice" to become an Autobot after Optimus gave him a personality that was likely to make that choice).
In both of these continuities he was Decepticon in name only, and his choice to become Autobot was crystal clear.
