Yup. I only know this from experience. We were trying to set up a retirement plan for one of the startups I'm involved with, which at the time had only a handful of employees. The company we were working with had great advice about how to best negotiate rules about Highly Compensated Employees and top heavy plans, and also offered a plan with lots of low cost vanguard mutual fund options. However, once they delivered the plan documents, I dug into the paperwork it turned out they were going to be charging 0.6% of assets under management each year initially (although this would have declined to 0.3% as the assets in the 401k plan grew).
Larger employers should be able to negotiate better deals, it just depends on whether or not they're incentivized to do so.
Now that said, if your plan is being directly administered by vanguard (not just providing access to vanguard funds), I think it's unlikely you'll find any egregious plan level fees in there but it is probably good practice to check anyway.