No.
The drain is not the determining factor for finished pan height. The curb (threshold) is the determining factor of this application since it always above the finished height of the drain. The pan liner should finish a minimum of 6 inches above the framed or (roughed-in) curb height. This height allows for the application of concrete base and finishes to be applied.  
Once you have the two pieces of liner cut square and laid flat on a warm hard surface (above 50°F), you must overlap one of the pieces over the other at least 2”. If you are seaming PVC liner use Oatey X-15, if the liner is CPE you will use Oateyweld. Fold back  the top piece of liner and wipe any debris or foreign substance off both surfaces with  a damp cloth and then dry thoroughly. Apply the proper cement for the application to both surfaces allow 1 to 3 minutes in hot weather and 6 to 8 minutes in cold weather, then join then together. Immediately apply pressure on the seam for 15 to 30 seconds with a 2x4 or equivalent. Leave this seam cure for 12 hours before installing, but after one hour there is good handling strength and you can move the liner. 
No. Thinset or tile glue (adhesive) should never be applied directly to the shower pan liner. 
The recommended thickness for this pour is between 2” to 3”. This is the minimal thickness starting at the drain, then sloping up and away from the drain at a ¼” per foot. This is not always possible due to curb heights. If this is true, pour as thick as possible and consider a higher quality cement which will allow for a thinner pour while maintaining strength. 
This depends on the quality of the cement products you are using and the minimal thickness recommended by that specific manufacture. The normal rule is ¼” thick starting at the outside of the flange, then the concrete is sloped up and away from the drain at ¼” per foot.
Oateyweld
Oatey X-15 Shower Pan Liner Adhesive
Oatey has approved the three following Liquid Nails products for this application. LN - 609 / Panel & Foam Adhesive  LN - 715 / Tub Surround & Shower Adhesive LN – 915 / Tub Surround & Shower Wall Adhesive
Mushroom Vent Caps can be attached to any vertical sanitary vent pipe, in order to keep debris from falling into the pipe. This doesn’t apply to septic tank vents which rise vertically out of the ground, and then turn down (looking like a candy cane).