The 6Ls are much more costly to overhaul and require an immense amount of updating and correction compared to a 4L80E...For example, the avg retail price for a 4L80E stock-to-mid perf build is about $2500-$3000 (transmission only, not including R/R) and the only real issues w/the 4L80E that have to be addressed at overhaul are worn boost valves (replaced w/Sonnax LB1 kit to prevent high line pressure), flimsy int clutch snap ring (replaced with 727 direct clutch drum snap ring), worn TCC regulator valves (replaced with Sonnax TCC valves) and some minor lubrication flow opportunities.
The 6L80, on average commands at least $4000 up to $5000 just for the rebuild (or reman unit). There's over 20 individual common pattern failure/weakness areas within that transmission that have to be addressed with updated/upgraded parts from the aftermarket (not to mention the torque converter)...Additionally, the cost to just replace a bad shift solenoid or pressure switch is equivalent to replacing the entire TEHCM (TCM) as all the solenoids, pressure switches and temp sensor is apart of one unified assembly which runs from $600-$1000 or so, depending on where you look)...If a 4L80E shift solenoid goes bad, it's $15-$20 to replace it. The entire electrical suite can be replaced for under $250.00 for all years 4L80E.
Lastly, the 6Ls command and control is a lot more complex than that of the 4L80E, requiring more extensive reprogramming and adaptation to integrate into a another vehicle where as 4L80E can be done with a basic segment swap for anything that took a 60 or a stand alone controller for a resto-mod application.
The above may not account for all of why the pricing is similar but it def explains a lot of it...
Cost + Risk should always be less than Benefit and the GM 6Ls come with a lot more overall sustainment risk than the 4L80Es for purposes of retro-mod swaps.