Religious thought provided the groundwork for all those things to exist.
Without European Christian alchemists trying to get closer to God, modern chemistry might not exist. Islam refined
ALgebra, invented trigonometry to make it easier for Muslims abroad to know where to face in daily prayers, and made significant advancements in astronomy such that we still use many of their names for certain stars. The number "zero" has its roots in Buddhism with "nirvana", which translates to "blowing out", as in a candle, and basically means "nothingness"; a concept that didn't seem to exist beforehand.
That's just the three major world religions. What more goes unrecorded from what the thousands of regional folk traditions contributed to the modern world, for better or worse, or is not remembered from our own broken and fragmented traditions?
For the record, by the way, agriculture was invented several thousand years ago, presumably in cultures heavily steeped in their own religious traditions, and they certainly did not have the modern scientific method, so what they created cannot be called a benefit "from science". Medicine is far older than that, and likewise applies. Modern technology and sensibility has certainly refined these technologies, but that's different.
As for whether any of the listed things are "benefits", that depends on how one chooses to look at matters. Allow me to play devil's advocate, as I do fully believe that the modern world is overall "better", at least as far as my own standard of living could probably allow, compared to times before. I certainly don't want to live in a world where video games don't exist.
Those things you listed certainly able to make overpopulation easier, which in turn produces more waste that piles up, and allows for rapid evolution of bacterias and viruses that makes it harder for our own immune systems to fight disease off. Not to mention the lack of adequate resources and energy to sustain the world due to the current world's dependence on a previously non-existent beaurocracy.
Even in the question of whether they've "improved happiness", that also depends on how happiness is defined. Near as I can tell, anxiety and depression are EPIDEMIC in the US right now, partially thanks to all the cyberbullying that inevitably comes with social media. Hardly what I'd call a "happy" society.
These were all caused by solutions to "unhappiness" problems, so what assurance do I have that any new solutions to these problems won't just cause more unforseen problems and make us all coddled and unhappy again?
My point to this devil-advocacy is to point out that you're argument is very biased as well: it's a bias of familiarity. It's impossible for an individual or small group to be even decently unbiased in opinion, judgement, and worldview. THAT is probably the MOST IMPORTANT benefic that the scientific method has given us which nothing else can: the ability for our collective knowledge to be as unbiased as possible. All those toys you mentioned are just happy side-effects of that.