"you can generally trust they run at big enough scale to have serious back-up" -- objection m'lud, assumes facts not in evidence. Plenty of big SaaS providers don't have decent backups; in fact, many of them weasel out of providing it by having somewhere in the fine print that it's your responsibility to have backups of the data held in the app (often this is coupled with a complete inability to export your data out of the app; yeah, awesome catch 22 there)
As far as doing your own backups of data stored on your own server, yes it's generally possible. However telling you how to do it in general isn't possible, because different apps/services require different procedures -- you need to run one tool for SVN, another for MySQL, and so on.
For commercial products, it can be very difficult to do a backup without their tool, because they've done something "interesting" with their data storage. Personally, any product that didn't come with the tools required to properly back it up would get sent back as "not fit for purpose" -- if you can't back it up, it effectively isn't managed. Charging extra for a backup tool smacks of extortion. One of the benefits of using practically-all Free Software.
EDIT: I think I misunderstood your question, and you're actually complaining about the costs of the backups provided by VPS providers. That's just standard marketing -- the low up-front cost of the system (so you can advertise your $0.89/decade VPS deals), then the eye-watering cost for all add-ons that people don't consider until they've signed the contracts (so you can actually make a profit). Pretty standard stuff -- I'm surprised you're not already familiar with it. Yes, you can use an off-site backup that's cheaper, although getting your data back onto the machine after a failure needs to be considered too.
Don't skimp on your backups, though. What most people consider to be "super-amazing" backup is, at the end of the day, about the bare minimum that's actually useful. I'm willing to bet that you've never restored a full system backup under time pressures from customers or bosses who are breathing down your neck wondering why you can't just press a magic button and have everything "restored from backup NOW!". Take some time while now, you've got a bit spare, to setup backups properly, because if you need to use them, they really, really do need to be super-amazing.