Synopsis and manuscript

It's probably more about her personality than a work flow sensibility. Some people are more anal retentive than others, and they all have their own process, however weird this looks to outside eyes. I've had stranger requests.
By the way, congratulations. This is a gold-plated question/problem, isn't it?

It's possible that she likes your writing, but still wants to be able to look at the plot as a whole without having to read the entire MS.

It's possible she wants to see how you see the plot arc and subplots.

She may use the synopsis to see if the "acts" (beginning, middle, end) of the novel seem balanced.

She might not look at it at all because she'll be so blown away by the MS.

Really, the only important thing here is: the agent asked for your full MS and a synopsis. It doesn't really matter why, only that you give her what she's requested.

The synopsis is a much quicker way to see about your plot than reading through the whole ms. I could see why it would be useful. Don't worry about it and be happy for the request.

Sat Nam! (literally "Truth Name"--a Sikh greeting)

Congrats! And don't worry about it.

Blessings,

Siri Kirpal