SuperPlus: This mode was released after the Indivision AGA MK2 was released. You can't expect me to support this and maybe more modes for all times in the future. I might do it, but at this point, we have "known bugs" to fix first. I'm happy to collect information, but I won't open a new construction site when the old one is not yet finished.
Other VGA modes: You can create them on your own, that's what the "VGA modes" menu item from the drop-down menu is for. Save your config and share it with others. There's myriads of presets in the world, and as keropi has shown, even openly available documentation is contradictory. I am supplying preset VGA modes as a reference for convenience, and if there's an error, I'm happy to correct it. However, I won't do the work of adapting everyone's config to specific monitors. That's what the config tool is for: You can do it yourself!
Pixel clocks: These are generated from the Amiga pixel clock by multiplying and dividing. As mentioned in a previous post, both multiplier and divider are whole-number values between 1 and 32 (both including). This sets limits to available pixel clocks. Since PAL and NTSC machines have a different chipset base clock, the outcome is also different, because PAL works with 28.37516MHz and NTSC works with 28.63636MHz. The config tool will display the exact middle (arithmetic average) between the two possible outcoming calues.
You're choosing 49.09MHz in the config tool. On a PAL machine, this will produce an exact pixel clock of 48.868MHz, and on an NTSC machine, it will produce 49.318MHz pixel clock.
Novacoder: If a screen looks "totally offset", then the screenmode recognition is obviously failing. For a proper bug report, please configure the OSD of the flickerfixer to "always on" and enable the OSD debug feature. This will display an additional line with information of the Amiga-screenmode such as number of lines, number of pixels and the H/V frequencies of the Amiga mode. These numbers are used for screenmode recognition. Compare them to the standard WB settings. As I wrote yesterday, there's still this mystery of Euro72 having two different screen sizes on two computers, which is not solved yet. If you have a similar effect even on one computer but with different pieces of software, we might get more hints on why this is happening. Note that the screenmode recognition is happening inside of the FPGA, and that's re-configurable. A new screenmode recognition entity can be put in a core update.