Doesn’t the intent of the programmer which is recognizable from source code lead to better protections?

No, it is not so. There are some advantages to source code modifications, but the disadvantages are dominant. Protecting object files can make an attacker’s analysis rather difficult, each flag might (or might not) carry essential information. Indirect jumps are far more easily done at the machine code level. The source languages are mostly aimed at clarity, rather its opposite, obfuscation. While White Hawk Software doesn’t use source code for its input, the customer can (optionally) guide the protection with explicit source code.