Fate Grand Order Masters, or Chaldea Agents, use command seals to both keep servants under control if need be but also to heal, revive exhausted servants, force teleportation, and other such. Its a tool to keep servants in action longer, or to give them magical buffs. For example


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Kadoc used his command seals to enhance Anastasia Romanov's casting abilities and to unleash her phantasm.
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Regardless of all the above it still is a carry over from the standard summoning system.