The "merged .lef" is the contatenation of all the input LEFs of the input blocks. The input blocks for

user_project_example

is just all the standard cells. The Input blocks for the wrapper is all the standard cells + the LEF that was generated for

user_project_example

as part of building

user_project_example

... and I'm pretty sure it's that last one which is 99% of those 1.3G.