It seems peculiar that to recognize, in my simpleminded reading, "making it more difficult for someone to get something" we cannot simply observe the parties involved but must consider the existence of some legislation -- wait, no, the intent behind the legislation. How do we even know the intent?

I don't think the lunch issue highlights it very well, as it is so mundane. A handicap accessible doorway highlights the issue much more IMO. In this context, we are talking about the SCOTUS interpreting legislation, and legislative intent is something that they typically consider. Of course, after the messy legislative process, it would be difficult to say that there is one clear intent to any law, but we don't make laws for the sake of having them. :)

I also think that for the word "restriction" to apply it should be meaningfully more difficult for the person to obtain what they want compared to when they had no interaction with the other party. I have plenty of lunch options, so if my boss declines to hold back a portion of my salary to buy me a tuna sandwich, it does not restrict my access to lunch (while reducing my income to buy tuna sandwiches would restrict my choices). This is true even if workplace tuna sandwiches are mandatory and other bosses provide them. I had the same access to nutrition before taking the job; if anything, the job helps me get what I want since the boss cannot control my spending.

And yet, the legislature thought the accessibility issue important enough to create the mandate. Of course, many disagree with the necessity of the mandate, but the issue at hand was: given the mandate, can an employer choose to opt out of specific portions of it on religious grounds? One might not feel that the access to some women's healthcare is a compelling thing to guarantee, but once guaranteed by law, the question becomes, to what extent can the employer refuse to provide it, and could this extend to other parts of the mandate, or other groups of people covered by it? (i.e. Can an employer refuse to provide dinner as well, or only refuse lunch to Jews?)

But would it not be better to maintain and encourage flexibility in what is covered, rather than forcing everyone to make the same choice? The fact that employers exist who are morally opposed to certain benefits suggests that there are also employees who do not want those benefits. By forcing some employees to pay for coverage for a benefit they do not want, their freedom is slightly eroded, their choices diminished, and diversity in society is reduced.

Maybe to some extent. But these are the difficult choices in a shared society. At some points our rights to equal treatment pale in consideration to the costs to ensure them, and at some points our rights to freely operate pale in comparison to the cost that others pay to ensure that freedom.