Well I remember quite well when Windows 95 became dominant and GT Interactive lost its publishing rights to Doom to a rival Activision. Soon after US stores received shiny new boxes of Ultimate Doom, Final Doom and other compilations like Doom Collector's Edition.

And these games were fully compatible with DirectX 1.0 sound and video cards through a convenient Doom port (Doom95.exe).
Happy owners of Final Doom, CD-ROM drive and Windows 95 could even run a game "natively" in SVGA resolutions 640x400 and 640x480.

So my question is: Can I run Doom in 640x480 resolution using GOG vanilla installers and without using any 3rd party enhancers (like zDoom and others)?

If you really want vanilla behavior in high-res, go for Crispy Doom instead of PrBoom+, because PrBoom+ defaults to its own behavior unless you fuss with its complevel configuration.

Not with the defaults. It was never set up for SVGA resolutions.