Why TimeQuest add clock constrain automatically?

It does that so at least "something" can be looked at. Otherwise it's kind of useless, and that aggravated users who were used to the old Classic Timing Analyzer which did a lot of things by default. You don't want to "overwrite" them. Create an .sdc file and add constraints. To use it, reset_design, which gets the netlist to write after being created before any constraints were added. Read in your .sdc rather than the default.