The pixel clock doesn't have to be the same as the color clock. In fact, it's usually higher. Remember that in a composite video signal, the chrominance information (whose resolution depends upon the color clock) is less important than the luminance information (whose resolution depends upon the pixel clock), so the color clock can be (and usually is) slower than the pixel clock. Color information is actually subsampled, as in JPG files.
If I were to design a video mode with NTSC output in mind, I would start with the color clock, which for NTSC is 3.57 MHz (aprox.) As discussed, you can have the pixel clock to be faster. Ideally, an integral multiple of this color clock. This way, some interferences such as "crawling dot" are avoided. This particular interference is present when the color clock is not in phase with the pixel clock, and this happens when both clocks are not depended one each other. An ideal design should use a single clock to derive both pixel clock and color clock for the NTSC encoder.
At the time, 4xNTSC crystals (14.31818Mhz) were usual and cheap, so I would pick my pixel clock to be that value.
As you notice, NTSC vertical resolution is 262.5 scanlines. NTSC interlace signal is not a big deal, but most retro computers use the vertical retrace period to trigger an interrupt, and game developers (at the time) would prefer this interrupt to have always the same period (measured in scanlines, or CPU cycles).
So, I would design with a 262 scanline picture in mind, and using NTSC progressive scanning (always outputting the same field).
Of course, all the scanlines are not visible. A safe approach would be to take 240 visible scanlines, which is, not by chance, half the standard NTSC resolution, and center them on the screen. That would give us an upper and lower overscan area of (262-240)/2 = 11 scanlines. Some of these scanlines are actually part of the vertical blanking period, so I would except the number of scanlines at the bottom of the image to be less than the number at the top of it, if you want to keep the pixel addressable area centered.
This, in addition to the 4:3 aspect ratio, yields a horizontal resolution of 320 pixels, so my screen resolution would be 320x240 with a border, or overscan area that would cover the rest of the picture. The standard NTSC resolution is 640x480. It's not a surprise that many standard resolutions among different computers have numbers very related to this one. Commodore 64, for example, but also CGA, EGA and VGA. Remember that early CGA adapters had a composite video output RCA jack, besides the Sub D 9 RGB TTL connector.
OTOH, A 14.31818 MHz pixel clock gives us more than 900 pixels per scanline. Therefore, I would divide that clock (now our master clock) by two to get a pixel clock of 7.15909 MHz. A scanline in NTSC lasts 63.5 microseconds. Using this pixel clock, the entire scanline is divided into 454.6 equal time intervals. Of course, we cannot use fractional time intervals, so I would use 454 ticks (clock periods) per scanline, for a total scanline time of 63.416 microseconds, which is pretty close to 63.5 microseconds, required for NTSC.
So we have 454 ticks in a scanline. 320 of them will be used to display actual pixels, while the rest of them will be used for horizontal blanking period.