In ancient days, absolutely.   Now the technology exists for the mats to assemble direct orders via computation and sensor arrays.  It took time for the creatures to accept those orders, but the mats wanted them to after all.  

So the mats can issue commands, bur more like a dictator than a hive mind.   ThE subtle effect mostly serves to make the creatures ideologally homogenous and subservient. 

As for the ecosystem thing, generally the Mats have a hard time competing,  so scorching the planet and introducing familiar life is a must.  Once entrenched the mats are able to properly grow and stifle any native life that managed to endure the cleansing.