Q: Why is this mod not applied to electric-powered machines?
A: There are several reasons. Firstly, the burner machines (those using chemical fuels) is quickly unfavoured by players, very often because of the extra logistics (having to lay fuel belts and to supply fuel). This mod will "revive" these obsolete machines back to use even in late game.
Secondly, the fuel consumption in burner machines consumes UPS (especially when used in batch, like the boilers and steam engines); while electric-powered machines do not suffer from this problem. So no real benefit to include the latter.
Thirdly, applying electric poles and grids is already quite UPS efficient. In fact, it is way simpler to use the perpetual engines on boilers, then let the perpetual boilers to supply free energy to power up everything.
Last but not least, most of the entities in game are electric-powered. Making a clone for each electric-powered entities is going to make your crafting menu also nearly double in size. Cluttering the crafting menu like that is going to annoy users, rather than provide real uses. (As mentioned above, placing perpetual boilers is much better than having perpetual variants of everything.)

Q: Why is this mod not applied to nuclear-powered machines?
A: While technically I can easily allow this (with very minor modifications in code), I wonder if it has any use at all. The fuel value of nuclear fuel and uranium fuel cells are very high, and vast majority of users have way more excess uranium-235 than they ever need. It is counter-productive to replace the already powerful nuclear reactors. Also, it would take a lot of perpetual engines to fit the power output of nuclear reactors, which makes it even less attractive.

Q: I feel the recipe of perpetual engines are too cheap/expensive. I feel the power output of perpetual engines are too low/high. Can you make it more like the S² Engine as what you referenced to?
A: S² Engine in Neon Genesis Evangelion is totally powerful, being able to power up the giant EVA units. The power output of it would probably goes much beyond GW range.
But comparing with Factorio world, there are a few concerns preventing such direct application... Firstly, the number of Angels (and their cores) in Neon Genesis Evangelion is less than twenty. In Factorio, there are no comparable aliens of such giant sizes (even with my other alien mods...) and also not possible to limit their numbers. To allow almost-vanilla players to enjoy such uses, the ingredients of the perpetual engines should be obtainable by killing behemoth biters and spitters. This single reason is enough for me to tune down the strength of each perpetual engine.
Secondly, no single entity (at least in vanilla game) consumes power at GW range. Providing an engine providing such huge power is totally an overkill. Another reason to tune down the scale of each perpetual engine.
Thirdly, because of the scaled down in needed power output, the material cost has to tune down as well. It should have a sufficient cost as it provides free energy once it started to work, but also should not be too expensive to discourage it from being used!
Due to above reasons, the perpetual engines are defined to be lite version of the S² Engine.
Yet, you may adjust the power output of perpetual engines in mod options (under "Options" → "Mod settings" → "Startup").

Q: Can the perpetual locomotive (and car) take the benefit from fuel acceleration and top speed bonus? Can you make it work with that?
A: This is a game limitation, so sadly no and no. Technically, the energy source is now "void", where the fuel properties are totally skipped.

Q: The perpetual locomotive (and car) do not take benefit from fuel, so we do not need them. Can they be disabled?
A: Sure, yes. Not only locomotives and cars, every entity type can be individually disabled through mod options (under "Options" → "Mod settings" → "Startup").

Full List of New (or Changed) Items

Intermediate Parts

• 1 power-related:
  • Perpetual engine

Recipes

• 1 intermediate part:
  • Perpetual engine
• Various machines:
  • Auto-generated, depending on mod options and mods being used.

Technologies

• 1 power-related:
  • Perpetual engine