I think it's very silly and in some contexts a bit dishonest to pretend that 40 man roster management consists of just writing down your 40 best players and walking away. Many (most?) teams don’t have full 40’s right now, and it’s not because every org only has ~37 valuable players and regards all of their eligible but unrostered prospects as org detritus.
Plenty of players who don't get taken in the Rule 5 would absolutely get snapped up if available in a trade or on waivers where they don't come with Rule 5 restrictions. Part of the reason they don't get protected is to reduce the risk of needing to waive/option them or someone else later. The question for Rule 5 protection isn't simply "is this a good enough player to keep in my org?" There's a finite number of 40 man spots, everyone in the league knows exactly how many there are, and using one for Rule 5 protection early in the offseason involves a long list of competing considerations.
What is the risk of another team committing a season-long roster spot to this player (as you said, very low) historically? In contrast, what is the chance that protecting them forces a riskier move when managing my roster later? Is Player A more or less likely to be claimed in the Rule 5 (where they can't be optioned) than Player B (who can be optioned) is on waivers? With my current 40 man balance, do I need rostered depth more in some places than others? Is this player's route to my opening day 26 more likely to be blocked, forcing an option year on my end that lowers their future control/value? And so on.
Most means of player acquisition are about value mismatches. Improving the Sox roster will inherently require acquiring players that have more value here than where they are coming from, but a player's value on your roster compared to their value on another is influenced by all sorts of things other than "they didn't think the player was good enough." Also, sometimes teams are just wrong in their evaluations entirely (and the wrong team isn't always the Sox!)
Garrett Whitlock (2.4 WAR last season) pitched in the playoffs for Boston in the same year they picked him up in the Rule 5 draft, and I doubt any fans watching were embarrassed by it. I similarly doubt they were sad about fellow Rule 5 pick Justin Slaten leading their bullpen in ERA in his first year there. Both guys are still rostered, not because Boston has had years of a desolate farm with no depth, but because they successfully found value where those guys' original teams didn't and found money spends just as well.
I don't think they (or anyone really) should feel bad for getting "too much" Rule 5 production. If anything, they should get bonus points because it freed them up to spend more capital in other ways, like grabbing Crochet.