Heyo, I'm the author of those changes.
A lot of changes were made due to code / entities being outdated or stuff being plainly unbalanced. Some of your requested changes are on their way to be incorporated however.
- hiding of fuel canister - For me was just another fuel with no benefitial value so I hid the recipe. However now thinking about the huge stacksize of the "liquid" diesel fuel, I re-added it now. But not making it stronger or anything. Just for use when you want a quicker refill.
- change of fluid waggon size - Was done for balancing, won't revert. No well written mod should break through adjusting those values o.O
- some waggons still missing wheels - I overlooked that, it'll be fixed.
- energy fuel unit not in fuel plant recipes anymore - Gonna be readded.
- small steam loco having realistic speed cap now instead of 300+ - Yeah that'll stay for balancing reasons lol
- circuit connection for fuel plant - Why not, think I can add that.
If you want some changes back, feel free to modify the code or write an adjustment mod yourself. Specifically for those adjustments it's fairly easy.