Going by e = mc^2, there's some truth to this. However, the simple fact is that liquid can be contained in a bottle, while energy (heat) will eventually leak out and equalize with the surroundings. Same principle applies here. Matter which is bound in a non-energy form will move through without issue. With energy, you are transmitting motion. It's not as tightly bound, and hence - you lose some.
Now, please don't forget but we are talking about MineCraft, a video game. I can store a fully charged RE-battery until I forget that I even have it stored, and when I find it four weeks later it will not have lost ANY charge at all.
I'm assuming, given the name, that your back story is that they are moving through a fourth spacial dimension, so while it is not exactly teleporting items/liquids/energy, it surely works just like a teleportation pipe.
And, of course, it is your mod, so you're free to do whatever you want to it. And you've done a damn good job, especially as you give us the config option to say "You know what, King Lemming, I disagree with you. Energy tesseracts should be free like birds, flowers, and bad advice about dating from your single friends." and change it.
Oh, question: You are checking for values between 0 and 100, right? If I have the time tonight, I'm going to change it to -100 and see if I can double my energy.
No, it is not. When you're talking about remote, compact builds - the Energy Tesseract affords you a HUGE convenience in space alone. That cannot be understated.
Sure it can, and it is actually because of another aspect to your mod that it can: Redstone energy cells can be moved by turtles. With some VERY basic LUA scripting, you can set up a turtle to grab a cell and put it in one ender chest, and then grab a new cell from another ender chest. If you have access to buildcraft gates, you can even get him to detect the state of the cell (empty energy store -> redstone signal, and then run a wire next to the turtle) instead of just timing it.
By doing so, which means three blocks, four if you count the redstone energy cell, and six if you count the redstone wire (RP2 jacketed wire works well) and buildcraft gate (on a pipe), and you beat your energy tax using a pre-existing system (again, thank you for those redstone energy cells. They are divine).
If a difference of a few spaces of blocks is really that important to you, or you are unable to do even basic LUA programming, then you get hit with the tesseract energy tax. After trying to convince people otherwise, and failing, I have come to accept that there are just going to be a lot of lazy people that don't mind being taxed for the slight (yes, slight. After the legwork, redstone energy cell moving turtles are not that much more complicated) bonus to space and ease of use you get with tesseracts.
At 100 MJ/t, and assuming you are using combustion engines, you are replacing nearly 50 blocks with a single block at a remote location. The extreme convenience of this warrants the penalty. Being able to centralize your power generation and then distribute it so easily is absurdly powerful, and 25% is probably even too low.
It's 25% too high for someone that has a better way. But yeah, it should be higher, maybe 75%, so people will be much more likely to give redstone energy cell moving turtles a chance. Getting people interesting in programming (even if it is LUA) is always a good thing.
I am sure everyone will feel really good about game balance when they make physical tesseracts less useful than Ender Chests (they're already more expensive and harder to make) and then everyone stops using them. We can all high-5 and go back to shying away from novelty.
Heck, that'd be horrible. I was wondering if anyone would say "Yeah, let's make item/liquid tesseracts require 25% off the top, too!" so I could turn around and yell at them. The balance should be removing the energy taxation (yes, I know this can be done in the config file), but King Lemming seems to believe otherwise. At least he has given us a way to change that ourselves if we want, and a way around that to those of us that can program.