I have read elsewhere of Emotiva products destroying Magnepan speakers (sorry, no source, some other forum about bypassing Magnepan fuses) I have not read of any other brand identified as a problem. So maybe there is some sort of incompatibility. Maybe someone needs to say it, no offense to Emotiva.
Another tweak for Maggies is to get some weight on the top edge of the speaker. Since the whole panel pushes in and out with low frequencies, and the panel is a large portion of the surface area of the speaker, low frequencies can start to move the less stabilized portions of the speaker, i.e., the top. Some custom stands try to stabilize the top edge of the speaker with braces. I have lived with bags of sand on top of my Maggies for months. What you will notice is tighter and stronger bass response. Especially with the lowest frequencies.
I have always wired out the fuses and tweeter attenuater jumpers, including on my MG-IIIs for 15 years with no problems. Mostly using Rotel and Anthem amps without issue. My understanding is the fuse is there to burn out in order to control heat building up in the wires during extended loud sessions. The heat will destroy the glue that binds the wire to the mylar film. Normally you can wire out the fuse and extra jumpers without a soldering iron or permanent changes. A better choice is to replace the mounting plate and binding posts to avoid magnetic/steel parts. You can also use the extra jumpers or replacement binding posts to bi-wire the speakers.
Replacing the simple crossover components (especially the capacitor) is also a big improvement. The crossovers only involve a inductor and capacitor on the lower models, so cost is reasonable. I have contacted Magnepan to discuss the crossover upgrades with them directly and they confirm it is a good place to invest in improvements.
Magnepan is definitely about bringing the speakers to market at an affordable price. They sound great out of the box. But manufacturers have to make choices about little items that save millions. Using a $1 capacitor instead of a $30 capacitor for the 2 caps in a LRS, would only increase the cost by $58. But if they sell 100k LRS speakers, they will save $5,800,000 in the cost of making the speakers without charging the consumer any more money, and they still sound really good. ALL MANUFACTURERS do this. Ford sells 1M pickups. If they save $10 on tires, they save $40,000,000 on one part.