What makes Smartfusion2 FPGA clamed as highly secure to ensure secure booting?
Nothing is absolutely secure.  There are degrees of security.  While higher security is often advantageous, there are usually tradeoffs to get it.  These can be higher cost, more difficulty in working with and doing development using the product, etc.

Storing the configuration inside the FPGA does provide higher security than having the configuration external and having to load it into the FPGA at powerup.  Whether that's secure enough for your purposes is something only you can say.  Meaningless words like "highly" are just that, meaningless.