To me it sounds like you are planning on doing a bit more math than what I normally find comfortable doing in Gnuplot. Have you considered using a tool as python with pandas?
It can be a bit of a learning curve, but this might be the time to learn a new tool..
http://pandas.pydata.org/pandas-docs/dev/10min.html
This gets you pretty close to what you want I think.
import pandas as pd
import matplotlib.pyplot as plt
dataSet1 = pd.DataFrame( [ [1, 2], [2, 6], [3, 5], [4, 6] ], columns=list('xy'))
dataSet2 = pd.DataFrame( [ [1, 1], [1.7, 2], [3, 3], [7, 5] ], columns=list('xy'))
dataSet1 = dataSet1.set_index('x')
dataSet2 = dataSet2.set_index('x')
full_dataset = dataSet1.add(dataSet2, fill_value=0)
print full_dataset
full_dataset.plot()
plt.show()
Gives you the output:
y
x
1.0 3
1.7 2
2.0 6
3.0 8
4.0 6
7.0 5

I didn't immediatly figure out how to define that add should check the x column, not the index when adding. I looked a bit at: Adding two pandas dataframes
and Redefining the Index in a Pandas DataFrame object