From 大辞泉:
###に‐おい‐て【に×於て】
に‐おい‐て【に×於て】
3 (多くは下に「は」を伴って)上の人物・事柄を強く指示する意を表す。…こそ。
This usage does carry some honorific weight, but perhaps more importantly it puts emphasis on what you're talking about, as opposed to something else.
殿 は どうか今後とも、自侭になさってくださりませい
You My Lord, keep doing as you wish
殿 におかれては どうか今後とも、自侭になさってくださりませい
As for you My Lord, keep doing as you wish
The connotation here being that, nirvana may be wonderful for some people, but not for the shogun. Therefore, as for him, he may continue being self-centered.