No, this is not a flaw in lock-screen security
What do you expect to happen if you were to do something similar yourself for valid reasons? Say, you are using a different computer and you ssh into your usual one and run the command remotely?
This is something that we actually do where I work, as we have odd screensaver issues and haven't figured out why - our issue blocks someone from legitimately unlocking the computer, so they cannot get back into it. They generally walk to the nearest computer, ssh to the one that is locked, and unlock it remotely, then walk back. So what you described actually happens at my work location all the time.
It is not a security flaw because your computer should do what you tell it to do, and to the computer your user account is you.
So this could be a limit to security, a case that the security measures do not cover, but not a flaw in existing security. That would be like saying normal fences have a flaw in that they don't stop things from climbing or flying over them - no, that's not a flaw, just a limit to their security, one which you can implement other measures for if it's a concern.
Real-world analogy
As a physical analogy, you are describing crimes where thieves steal your house key when you're not looking, take it somewhere to have a copy made, then put the original back before you notice... and you are suggesting that this is a security flaw with keys that can be solved by banning key-copy services. Not that this would ban key-copying, as it would ban only the public service... people would still copy keys, just like people would still sneak malware onto your computer if you walk away with it unlocked.
How to increase security
The Bluetooth proximity unlock you mention sounds excessive, but if this is truly a massive security issue for your place, then that is one of the better ways to go. You probably don't even need to develop this yourself, as there are probably products which do this.
To continue the analogy, the Bluetooth proximity thing would be like having an alarm that triggered if your house key was moved too far from you. That would require thieves to do their work behind your back with you nearby; still possible, but more difficult.
Some other security methods might involve training people to always lock their screens when leaving their desks, or even further having a policy which states that all computers must be locked if the user is not within sight of it.
That is actually a policy where I work. If I walk away from my desk even just around the corner for 60 seconds for a coffee (which is in ear-shot of my desk and I can peek around the corner at it), and if I forget to lock my computer while doing so I can get into trouble. It is part of our security policy, and people are reprimanded for it.
Another thing to do would be reduce auto-lock timeouts. If they are at 10 minutes now, put them at 1 minute or less. That can be annoyingly short when reading a page of text, but if it's a big enough security concern then people need to just deal with it.
Reducing auto-lock time will stop your stated scenario from occurring in the cases where someone happens to walk by a few minutes after you walk away and see you're gone and your computer is unlocked. The vulnerability will be available only to those people who are actively stalking you and are ready and waiting to pounce on your user account seconds after you walk away.
Take-away
100% security is impossible
No matter what you do, it will not be possible 100% to stop what you describe. Someone can subvert a computer even if its user is present. Someone could stop by while you're at your desk, supposedly just to talk to you.
Hey, is that the ABC file you have up? Can you scroll up so I can
point something out to you.
[slips USB drive into computer while you're staring at monitor]
@Paŭlo Ebermann commented "Your attacker doesn't even type the command for the malware, his USB device can just pretend to be a keyboard too." Very true, thanks for making the point even better. Deleted extra unnecessary steps.
And that's assuming that you couldn't just get someone to run your malware themselves. "Hey Bob, can you try out my newest version of our software? I think I got the bug fixed." (Bob then runs the software he is developing with Tim, not knowing Tim put malware in that specific build of it, then Tim deletes it in 5 minutes)
That's all it takes, then your computer account is already 100% compromised, even while locked.
It is practically impossible to protect a user account from the actions taken by that user account, and
it is practically impossible to guarantee that the actions taken by that account are all exactly what the account's human owner desires.
To go back to the analogy...
I used the key example because of your specific lock-screen case, wherein the lock-screen is the key. But, as pointed out by commenter @David Z, the problem is actually worse. By analogy, the key theft is a minor concern as you already have people living in your house without you knowing it, and they are doing whatever they want all day while you are gone, even though your door is locked.
If you're fortunate they will leave a mess and you'll come back to a home that looks obviously ransacked. "What??? If I'm fortunate?" Yes, because the worst case is far worse. They could live in your house for years, always picking up after themselves, so that they can keep stealing from you and living in your home for years without you even noticing. Or even using your home as a hub for criminal activity, like drug sales or pawning stolen items.
That would be like your office's computers all having key-loggers, remote control software, constantly downloading all your company data, or even being consumed as part of a botnet such that those computers could actually be engaging in illegal activity every day without you even knowing. All while the door is still locked.
I just stumbled on this great XKCD joke and it reminded me of this answer, so I've added it. Notice the 5th "security vulnerability" from the bottom.
gnome-screensaver-commandwould need authenticated access to your screen too.