Part I - by now vs now
These sentences may all be uttered with bare now, no by, but they will mean something slightly different.
Bare now simply describes the present state. By now focuses on the process by which the present state was achieved. It emphasizes change of state over time, in the course of the process, and it leaves open the possibility that the process will continue in the future.
By now the desk should be looking significantly tidier! ... This emphasizes that the disk looked significantly less tidy in the past—and may look even tidier in the future as the process continues.
By now, the failure of regulators to contain dangerous forces should be well accepted. ... This emphasizes that the regulators' failure was not 'accepted' in the past, but has come to be accepted over time.
By now I own some forty copies of the magazine. ... This emphasizes that your process of acquisition took some time, and leaves open the possibility that you will acquire yet more in the future.
By now the blue of twilight is glowing. ... Without more context, it is difficult to say why the author wants to focus on the change over time; but just for instance, he might be a cinematographer describing the changing quality of illumination he must capture ... and we must replace the polarizing filter with a two-stop ND grad. (NOTE:I made that up. If a Real Photographer wants to correct the technical details I will be grateful.)
He used leverage, but by now applied concerted discipline to contain his risks. ... This emphasizes that he was less concerned in the past to contain risks, and leaves open the possibility that he will be yet more disciplined in the future.
Part II - tense change A change from simple present→simple past changes only the time reference: you assert that the eventuality obtained in the past rather than the present. Now or by now have the same significance as in the present, but refer to a past rather than a present Reference Time: they might be replaced with (by) then.
5. is already in past tense. 3 and 4 are pretty simple: you just change the present-tense forms (3pr, 4pr) to past-tense forms (3pa, 4pa):
3pr. (By) now I own some forty copies of the magazine.
3pa. (By) now I owned some forty copies of the magazine.
4pr. (By) now the blue of twilight is glowing.
4pa. (By) now the blue of twilight was glowing.
But the two with should are tricky, because that past-form should may represent either a realis or an irrealis. I'm going to cast these as reported speech so the time references are clearer.
1pr. (Tom reports that) by now the desk should be looking significantly tidier!
2pr. (It is clear that) by now, the failure of regulators to contain dangerous forces should be well accepted.
With a realis, should is identical in the past tense, so if 1pr. means “he is confident that the desk now looks tidier”, the past realis version 1pa-r will mean “he was confident that the desk now looked tidier” and will be expressed this way:
1pa-r. (Tom reported that) by now the desk should be looking significantly tidier!
But if 1. means “he feels the desk should look tidier than it does”, the past irrealis version 1pa-i will mean “he felt the desk should look tidier than it did” and will be expressed this way:
1pa-i. (Tom reported that) by now the desk should have been looking significantly tidier!
The corresponding versions of 2 are
2pa-r. (It was clear that) (by) now, the failure of regulators to contain dangerous forces should be well accepted.
2pa-i. (It was clear that) (by) now, the failure of regulators to contain dangerous forces should have been well accepted.
Part III - perfect recast A change from simple present→present perfect is quite different. (Again, I’m going to skip #5, which is in the past tense rather than the present; if you find it presents issues distinct from those addressed here, I’ll be happy to address them in a separate question.) The two versions without modals have significantly different meanings than their simple present versions.
3prpf. By now I have owned some forty copies of the magazine. ... This implies that you have disposed of some copies, which is not the case with the simple present version. This is an implicature, not an entailment—it may be cancelled—but there is no reason for you to employ the present perfect unless you in fact no longer own some of those forty copies.
4prpf. By now the blue of twilight has been glowing. ... This falls very odd on my ear. Without now or by now the sentence might (just) be employed to report a previously unobserved recurrent phenomenon: the blue of twilight used to appear dull, but for several nights recently it has appeared to glow. But with either now or by now it demands a complement defining the other end of the timespan: By now the blue of twilight has been glowing for several hours. (Perhaps this is that same videographer shooting in the far north, where twilight continues through the night in summer!)
As for the two sentences with should, you know that these cannot be literally recast in the present perfect. There is no such thing as perfect modal, because modals are defective—they have no past participle to enter into a perfect construction. The closest you can get is a modal perfect, in which the modal takes a perfect construction as its complement:
1prpf. By now the desk should have been looking significantly tidier.
2prpf. By now the failure of regulators to contain dangerous forces should have been well accepted.
I have already indicated what these signify in an irrealis context (see 1pa-i and 2pa-i, above). If the should bear a realis significance, you have the same problem as with 4prpf—you need to pin down the front end of the timespan.