[Review updated January 3, 2021]
Delighted to confirm that, with the balancing tweaks and the information in MonoXD's review, the Eggman boss fight is a lot easier than I remember. Use Protect once at the start of the fight, save your magic attacks and skills for when the robot opens up to fire its laser, and you should win. And unlike the fights in Episode 5, where you have absolutely no margin for error, Episode 6's fights do actually offer you a little leeway.
The level of improvement between Episode 1 and Episode 6 is something to behold. While some of the backgrounds appear to have glitched and don't look right, everything else still looks okay, in contrast to the first four episodes and parts of the fifth, which seem incredibly dated now.
Looking forward to playing Episode 10 once I finally make my way through the rest!