Hobby Lobby isn't mandated to offer their employees a 401(k) program, it's an option they choose to make available. The issue here is that Hobby Lobby doesn't want the government mandating something that they feel opposes their religious beliefs. Retirement plans don't do that, and trying to find a fund that has 0.30% holding in a company that owns a company that makes an abortion pill, seems like a reach.
I don't manage Hobby Lobby's qualified plan holdings, but I do manage companies close in size. In my 25+ years in this industry, I've never seen an a la cart plan made available to a mid size company. They get options, but it's typically "do you want this plan with 35 fund, this plan with 40 funds or this plan with 45 funds"? Employers typically offer the best available plan for everyone. But the don't get to build a plan specifically with the funds they want. If that's the kind of plan they want, then they wouldn't be offering a 401(k) at all.
What I find kind of funny with this "Landmark Case" is that the ruling will affect nearly nobody. Most companies aren't going to purposly try to make their plans look less inclusive (as a good retirement plan is a draw to future employees). The IBMs, McKesson's, Proctor & Gambel's of the world aren't going to lose a minute of sleep over this. This helps the small companies, the companies that weave their religious beliefs into the fabric of their business. They're the one's who win. It doesn't really "hurt" anyone.