I don't see how adding the SE slips only will worsen the factory lean condition. Same amount of intake air and same amount of fuel added. Same AF ratio.
Its all about volumetric efficiency my friend.
Any time you alter the Harley Davidson engine whether it be free flowing exhaust, intake or cams, you alter the volumetric efficiency or amount of air that the engine is able to pump through at any given rpm.
Free flowing exhaust reduces back-pressure which allows spent gasses to flow out of the engine easier, thus the engine is able to flow more air into the engine compared to the air flow with a stock exhaust.
The fuel injection system used by Harley Davidson is essentially a speed-density type system.
In simplified terms, it works like this:
Based on a given intake and exhaust system, if the air temperature and pressure is this number, the throttle position is at this angle, and the engine is at this rpm, according to the look-up tables or calibration inside the ecm, there must be this much air flowing into the engine therefore it needs this much fuel.
This would be considered open-loop mode when fuel metering is based solely on sensor inputs and look-up tables and the ecm is not using feed back from the o2 sensors to monitor where the actual fuel ratio is at.
In closed loop, the ecm does all these same calculations based on sensor inputs and look-up tables but then is able to see how close it is actually getting the fuel mixture and make small adjustments as needed based on the feed-back from the o2 sensors.
I am still learning about the Delphi system used on Harley Davidsons and could be wrong but I believe the engine typically only operates in closed loop during part to mid throttle cruise conditions.
By re-flashing the ecm, you can change the look-up tables or calibration so that the ecm calculates fuel flow for the correct volume of air going through your engine based on the type of air intake, exhaust system etc. that is installed on your motorcycle.
True, just adding slip on mufflers should not impact air-flow to the same degree that adding a stage one air intake system would, but even small changes in air-flow will throw the calibration tables off, especially when the factory calibration is already on the lean side in order to comply with epa regulations.
Again, this is a bit of a simplified analogy but hope it makes sense and takes some of the mystery out of fuel injection. Cheers!