What you say about the holodeck could make sense, but, for whatever reason, they frequently make a point that things can't be carried out of the holodeck... except when someone gets soaked in the holodeck and walks out wet meaning they did incidentally take something out of the holodeck.
Of course, even if very large and with pretty big doors, probably not big enough for any equipment they might need. Since the replicator technology is like the transporter tech, it would stand to reason they could just replicate something to anywhere they need, without having a dedicated area where replicator stuff must come from. Of course then you get into why do they even have cargo room transporter pads, or transporter pads at all, why is 'site to site' transport the exception rather than the norm? Why do they have to 'go to the replicator' to get their food instead of it materializing right on their table?
Then you get into Voyager where they got extra weird about things being "holographic" as a kind of whole distinct state of being...
Well anyway, short answer is repeat to yourself 'It's just a show, / I should really just relax.
But yes, the safety protocol off for some actual experiment is ok...