So how the situation is better if both MegaCorp and small startup are using each other opensource code with just the BSD license (with no patent grants)? megacorp can still sue the startup for patent infringment and destroy it.

If you assume that MegaCorp is evil, the startup has no life whatsoever, whatever open source license is picked. If instead assume that MegaCorp is good, the patent grant has a positive effect on the ecosystem.