This problem with 256 lines modes & ArcadeVGA is a classic one and in fact is what got me into the "modeline science" back in 2008.
The problem, as you have perfectly described, is that 256 lines modes are defined with a too short vertical back porch. Too short for a standard arcade monitor (although maybe enough for a multisync monitor such as the WG).
A standard arcade monitor needs at least 16-18 lines for the back porch, because its electronics are similar to the ones in a standard NTSC or PAL TV.
The ArcadeVGA cheats here by using a shorter back porch, in order to keep the horizontal frequency below 16.2 kHz while reaching a vertical frequency quite close to 60 Hz. But this causes problems, like visible retrace diagonals and missing lines or compression on top of the screen. This happens because the monitor doesn't have enough time to move the electron beam back to the top of the screen (this takes around 1 ms for a standard arcade monitor).
As you noticed, when using the arcade_15 preset in GM, which is limited to 16.2 kHz, you only achieve 58.48 Hz for 256 lines modes. This is because it is calculating the modeline with the proper back porch, so the vertical refresh goes down as expected.
Now what if you want to use 256 lines at 60 Hz and still get all the lines on the screen? Because you need 16-18 lines for the back porch, you must reach the 16.7 kHz horizontal frequency. This is what you get when you use the arcade_15ex preset in GM. You have done this manually by tweaking the modeline with Powerstrip.
Whether it's safe or not to use 16.7 kHz for your particular monitor, I can't give you an answer. I can tell you that I've been using this frequency all the time for my vertical games with a couple of Hantarex MTC 9100 monitors that I have since 2008 and so far so good. But that doesn't mean that you won't break your monitor by doing so.
In theory the more you move from the typical working ranges, the more you stress the circuits and increase the probability of a failure in the long run.
In the case of the MTC 9100, its service manual says it has an operational range of 15.7 +- 0.5 kHz "adjustable". This represents a "window" of 1 kHz, and adjustable means that it has an H-freq pot which you can adjust (obviously), so this 1 kHz window moves up or down. In my experience, there seems to be a maximum value for the adjustment, which is, exactly 16.7 kHz. Because of the 1 kHz window, this also imposes a minimum usable H freq value, in this case 15.7 kHz. This means that slightly lower frequecies that usually work, like 15.625 kHz will roll when using this adjustment, so you must enforce all modes to reach the minimum horizontal frequency (all this is automatically done by GM by assigning the proper frequency ranges).