My Head and The Mikveh

I've put a thing of some sort on my head for brachot for years.  And then I got married, and started going to the mikveh.  One makes a bracha in the mikveh, so of course, I ask for the shmatta (rag/cloth) they keep for the purpose, beforehand.  I've just gone along with a general sense of consistency.

However, it's been brought up that there are other differences.  In other words, I am not usually otherwise naked while making those other brachot.  Given that difference, does it still make any sense to cover my head?  Conceptually, the question is- are head-covering and body-covering related?

When it comes to real experience, I don't know if the theory matters.  I feel awfully strange about the idea of not having that shmatta there, for all that my body is covered in nothing but water.  I haven't looked at the halakhot yet, but for myself, the thought of carrying out an important mitzvah with a completely bare head just bugs me.

Maybe it's that covering my head has always had a spiritual component, for me, while covering my body has to do with other people.  My clothes aren't relevant to God, but having a head-covering is about acknowledging God's presence, and reminding myself of it.  It's about recognizing that God is watching.  In other words, that shmatta is a kippah, not an "I'm married" sign.  Maybe then, if that sort of head-covering wasn't part of your practice before, it doesn't feel so odd to make a bracha without it.  But for me, I really connect to that symbol.

How do you feel about it?