all high output alternators worsen fuel economy. it takes more energy by the engine when the alternator produces more current. alternators convert mechanical rotational energy into electrical energy + heat.
because more energy is used to spin the alt, engine power delivered to the flywheel also suffers.
so the answer is yes, performance and fuel economy worsen when you increase current production by the alternator because the engine works harder to spin the alt. many people with smaller engines have experienced the engine stall during high current demands on a H.O. alt.
because high output alternators are capable of producing more current, they are capable of demanding more work done by the engine.
if you disconnect a plug with a CANBUS connection you will get a CEL code/light. You won't get rid of that code until the CANBUS connection is re-established.
driving around with error lights isn't a proper installation and the dealership will have an excuse to not warranty anything connected to the associated system.
finally, bypassing the PCM control of the alt will greatly noticeably fuel economy and performance. the PCM uses the alt control to balance power, fuel economy, and current output of the alt. the alt is turned off to save fuel and boost acceleration. If you bypass the fuel saving methods of a stock alt, you'll see a 2-4 mpg decline, all else equal. You can verify this by driving around with your headlights on (typically forces the alt to stay on). If you bypass PCM control and increase alt size, i predict you'll see a 5-7 mpg decline (at times of high current usage).