Retirement benefits vs. better salary/health insurance

I’m a research scientist and postdoctoral fellow in a US government lab. Currently, my position is funded through a DOE-run organization as an educational/training position. The salary is good for my field, but benefits are a little slim, and the pay is considered un-earned income (fellowships/scholarships), so it does not qualify for tax-incentives like IRA contributions. My supervisor has switched my funding mechanism to a private govenrment contracting company (McNeal) starting in september, instead of the scholarship/fellowshio mechanism.

Here’s the rub. With the fellowhsip, I get an additional personal health insurance stipend on top of my base salary that covers the optional insurance plan they offer, which is great (low-deductible, low co-pays, dental, vision, etc.). As a contract employee, insurance premiums are deducted from my base salary (pre-tax), so my take-home actually ends up lower than with the fellowship. Plus their insurance plans are all sub-par compared to my current situation. Their best plan costs the same as my current premiums but with 2x my current deductible, ~2x the OPM, less dental coverage for an extra premium, etc.

Only real plus I see to the contract position is that I can start my first tax-incentive retirement savings (at the ripe age of 33) with non-matched 401K and IRA contributions, which my current income does not qualify for. I can also opt into short- and long-term disability insurance for pretty cheap, which is kind of nice. I’ll make enough that I theoretically could max out the 401K contributions, though I’m not sure that I would want to.

My question: Is this new funding mechanism really benefiting me over the old fellowship mechanism if I’m trading a lower take-home (~$2000 less after insurance premiums deducted) and a downgrade in health insurance for the benefit of tax-incentivized retirement savings? My supervisor feels like he’s doing me a solid by switching me to this new contractor position (because it’s more expensive for the lab), but I’m worried that it might actually hurt my overall bottom line. The contract has already been awarded (I could not see the benefits package until it was), so this question might be moot until my next renewal anyway.