Fundamentally it comes down to this: everything you're describing here is the result of policy decisions. People need to have places to live and work. The locations and dollar values attached to those items are the direct result of whatever policies are in place. You can sit back and say, "behold the reality, such as it is, we can fight for minor changes but this is just fundamentally the way things are" or you can recognize that literally everything, everything variable, everything that happens is actually the result of decisions the government has either made or chosen not to make.
It is certainly not unrealistic or a fantasy or naive to demand that the city take a far more aggressive and active interest in populating urban nodes that are already dense and covered well by transit with housing and street level commercial space. The reason that so much of what people love (and are accused of romanticizing) like small shops and the like is not the result of some law of nature or inevitable process of the Internet, but again, the result of policy decisions that have been made over decades that have led to rapid and continuous increase in inequality and centralization of power. It's not that nobody wants the mom and pop shops and prefers Starbucks to local cafes, it's that with a combination of ever increasing rents and every increasing power of big businesses, a small store cannot possibly compete. As each one goes out of business, that only further concentrates wealth and power in the competitors. I'm not arguing for state subsided bookstores but people take for granted that the processes we all lament are not actually inevitable. More breaks and much stronger regulation and tax and land use policies actually could, and once upon a time did, mitigate these effects. These things can be changed. And what is concerning is the degree to which people just wave their hands say this is just the way it is, and we simply have to count our blessings that we live in a city rich with beneficiaries of big business/tech/biotech. As you say, these process are indeed all connected. It's not simply about "big pharma" per se, since there are certainly other labs that are smaller (I assume this is the case, although I also imagine you're going to see very little of that in Boston, either), but also about asking harder questions like--who gets these jobs, where will they live, how does this impact the local economy. A major problem is that public officials like to trumped "jobs" regardless of what those jobs are. I would be most concerned to know, do these jobs offer a realistic opportunity for people who are born and raised in the city? Or are most lab jobs given to highly educated transplants from outside MA, whose high salaries only further exacerbate the local housing costs? And, while we all worship the invisible hand of the market, worth also stepping back and understanding that the success of a massive portion of the biotech industry is part and parcel related to the extraordinary expansion of healthcare dollar expenditures in the USA, which in contrast to literally every other western democracy, has not led to any increase in $/mortality improvement (we are now alone on that curve which for us is actually going down, not up). Sooner or later, the healthcare piper will have to be paid, so it might be nice to have some leadership in office to wonder whether or not we might not want to stake the whole city's success on a likely eventually sinking ship.
The problem with systems is they act differently than the individuals of which they are composed. Few people out there are actually evil and this isn't about scapegoating one person, one industry, or once demographic. But the system ends up moving in the direction it's going to move in, and that's shaped by what is and is not regulated. It's about understanding that elected officials and the economic, labor, and housing policies they implement or dont implement have deep impacts on the local ecosystems. It's not impossible to change these things.
This issue isn't just about one lab in Kenmore. Agreed that creative integration of different uses in urban nodes is good. But we are facing a trend that seeks to fill in much of the space between Longwood and Kenmore with labs. And this will have an effect. Go to Kendall Sq and look who's walking around. And look who can afford to live there. Is Kendall a regional success? Sure, I suppose, but there have been many negative impacts as well. Not scapegoating Kendall alone for high housing costs in East Cambridge, but when it's trendy to live in places like that and you've got a huge industry of life sciences execs flowing in, it will have an effect. So again, just saying "life sciences=more jobs and healthier urban ecosystem" is somewhat disingenuous. Always the question: but for whom?
