Bending the lift link was likely an anomaly, your understanding is correct that the float should allow the whole mower to move up, but perhaps there was another outside factor restricting things. Also the adjustable lift links are sometimes just a tube so it would be significantly weaker in compression (buckling).
As for the reason I use the side chain, one of my fields is very bumpy and I haven't had the chance to level it out yet. This allows the mower the go freely into the ruts and back over and not miss odd chunks of grass. It also evens out the pressure on the rear roller and its bearings.
I also drop the 3ph lever to float and the top link controls the height of the front of the mower. I don't have position control, so using the alternative of using the 3ph to control the front height (and perhaps a chain or floating lop link) would not be unrepeatable without check chains or something else to consistently set the 3ph height. The top link does a fine job of this and I can find adjust right from the seat. Also, my flail does not have a floating top link so that's another reason for me to run this setup.
I don't get any scalping from the skids unless the ground is majorly unevening, which is the result of the ground and not the mower set up. I did some quick analysis and concluded with either setup there is a chance to scalp. With top link setting the front height it can scalp when the tractor's front wheels go into a dip or start down a hill. With the 3ph arms setting the front height its when the tractor's front wheels go up a hill or bump, this lowers the 3ph arms and dips the front of the mower. Properly adjusted skids will avoid any scalping from the blades but the skids themselves might especially during turns.