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Hmmh, No I don't think you can make the idle power consumption go down. Sure, you got to set the right options in the BIOS and Linux. But there is a baseline and that's with which chipset the mainboard was designed and what kind of components they chose.
And there's the efficiency of the power supply. Usually they're built to have a certain degree of efficiency (>80% or >90%) but that's measured at a certain percentage of the maximum power draw. They're not at all that efficient at 40W draw. You'd need an expensive PSU not to lose additional efficiency at low power. And generally they don't come with a standard PC.
So you'd probably end up replacing half of the components of a standard PC while making it more power efficient. And I don't think that'll be cheap. You better find something that's already designed to factor that in. Sadly it's not what they print on every PC. You have to look for that info and sometimes it's buried in some PC magazine forum or on Reddit. Sometimes they have additional tricks to squeeze out a tiny bit more, but you better be fine with that number.
I think mostly it's about the mainboard. Most of the time there are some chipsets that are known to be more power efficient than others. But I'm not up to date anymore and can't give any good recommendations.
If you want it cheap and most power efficient, generally the advise is to use an old laptop. They're made to idle at like 10-15W. But you won't get any SATA ports that way. You'd need external HDDs and connecting them via USB isn't really super reliable. It's frowned upon to use a setup like that for RAID or advanced things... But it's how I started back in the day.
With the upgradability it's always the question. That's an additional requirement that makes it more difficult. If it's an old machine you could end up needing to replace most of it anyways, since you need a new mainboard for a new CPU and along with that the next generation of RAM and then you've replaced most of your computer anyways. I'd say there is a limited window of opportunity when upgrading makes sense. But if you're buying an old machine it may not always be a good idea to make it a requirement.
To follow that up: 45W isn't that bad. Depending on where you live, I'd say it's worth it if you get something out of it. (Be able to fit the HDDs, upgradability, ...)
Ultimately you'd need to do the maths. Check what it costs to afford an additional 20W of power in a year and whether you should spend that money on better hardware. If my maths is right, 20W for a year at a high price of 30ct/kWh is about $52. So there isn't that much to be gained. And your electricity might be considerably cheaper anyways.