For me VIA MVP3 has not been more stable than ALI V, in fact my experiences have been much better with ALI + K6-2+ or K-6-III+ compatibility, even on boards that did not officially support them with some bios tweaking. Stability has been the same, they are pretty stable systems when the mainboard is well made. Ali performs better in some tasks/games, and VIA in others, and for me, ALI + Windows 98 is easier and more reliable, as there are only a set of final drivers and they work straight away, with VIA, there are tons of 4 in 1 versions, ones containing VXD drivers, others WDM, or a mix, and i suffered some VIA inconsistencies with AGP graphics cards that i had to solve trying different versions of the drivers. For VIA, newer drivers does not mean better drivers.
The problem with ALI is that it seems the ALADDIN V chipset might have been cheaper in its age, so there are a crap load of low quality chinese cheap motherboards out there using them. They were bad, with zero support, bad quality control, and non-existant bios updates, and some are dieing now because of bad capacitors. This is bringing bad reputation to ALADDIN V Motherboards, but it is not ALI's chipset own fault. There are very high quality ALI motherboards out there, like yours.
Right now, the Aladdin V motherboards I still keep are the BCM VP1541, also known as the Diamond Multimedia Micronics C200 (ATX), and a Jamicon 566-A-AT (Baby AT). They are both well made boards, hightly overlooked, and still can be obtained for a decent price.
The BCM VP1541 does EVERYTHING the Aladdin V platform can offer; Official K6-2+ and K6-III+ support, Big HDD support, a lot of settings for everything, etc. The Jamicon is a bit more limited, it works with the K6-2+ / K6-III+ but External cache must be disabled in BIOS (no big impact on this processors which have internal L2 cache), and it does not support BIG HDDs, but i built around it the system i am most proud of, using an old 2003 Asus barebone case modified to acomodate the Baby AT board where it fits very tightly, a Voodoo 3 (a Voodoo 2 does not fit), a Promise Sata controller, a Samsung SSD, a Sound Blaster AWE64 (A good SBPro or 16 does not fit), Floppy and CD-ROM. The system is very, very compact, stable, fast, and compatible with almost everything DOS/Win98. In fact sometimes i wonder why i keep thinkering with Pentiums, MMX, II or III when i already have the perfect system for me for that era of games. Curiosity i suppose.
I would suggest you to have the most important parts ready at your desk, and try both motherboards with the components you want to use, and see for yourself which one behaves better or you like more. Also, you can solder wires at the back of the dip-switches and install a front panel just like they were standard jumpers, if you do that just let the switches off at the motherboard and use the front panel switches as you like.
Anyway as you want to use a K6-2+/K6-III+ processor, that front panel switches will be really unneccesary, as this processors multiplier can be controlled using command line tools or windows apps. You can make them run at 386SX speeds or at full 600Mhz with a single command line, i have never seen a K6-2+ or K6-III+ that is not stable at 100x6 with the right voltage, they run pretty cool, and passive cooling with custom made heatsink is feasible.