Pessimistic with direction of academia-industry project I am a recent fresh graduate who came from math and physics. Recently (&lt; 4 weeks), I've taken on a junior research role in a research institute within a University.
This particularly university - and those in this country - have extremely strong collaborations with industry partners so work in Universities in this country is divided into pure/ fundamental research and industry-driven research. The University houses corporate research labs. 

The project I am working on right now is in the area of air traffic. I report to a fellow (academic title) who comes from industry who is only focused on research in operations/ convincing stakeholders and sponsors.
Research because everything he proposes and investigates are qualitative and conceptual without any justifications with mathematics in an area which presumably requires mathematical models to validate ideas.

Granted that I have been in this role for &lt;4 weeks, I am miserable and I believe I will continue to feel so.

1) 
I believed I was overpromised.
I was promised that I would be working alongside professors to develop new mathematical models for air traffic. 
It turns out I am the only person from math and physics. The rest are from engineering or industrial design field. 

2) 
Much of my time would be involved with producing white papers and policy recommendations for management of future air traffic

3) I am pushed to pursue a PhD (comes with scholarship) which, with internal discussion, would allow me to move into a PhD program even with an average BSc grades since the director of the research institute is the PI for the PhD program. 
However, my thesis would have to be in the area of air traffic.
My interest is in Abstract Algebra, Topology and Quantum mechanics and I'll like to pursue this in a year or two time when I return back to University.

4) The fellow I report too is really a project manager in disguise. Every discussions with him mainly revolves around stakeholder expectations and  targeted objectives. 

A good case scenario is this: He engages a visiting scholar who has done a PhD thesis in air traffic modelling, look to see how the idea in the thesis could be extended to specific circumstances (without much modification to the mathematical model in the thesis) for national interest before suggesting a feasibility write up on why this works.
From here, it is already obvious that nothing of substance could be published in respectable journals. 

I am afraid that my current research role will not provide me with a stronger exposure to math or physics in the fundamental sense.

What is the best course of action?
My answer is rather a statement about what not to do rather what to do: 

Do not do a PhD in a field you are not interested in. And do not choose a field of research for your degree just because of convenience (offer/opportunity). I cannot emphasise that enough. 

In addition, switching topics drastically after a PhD is very difficult. It is possible, but I have seen it rarely succeed. 

Usually, people start with a related topic and then drift away in the direction they are interested in. However, drifting from ATC to Topology/QM does not look obvious; Quantum airplanes? Topological path planning? Braid groups for flight patterns? Perhaps...