The current Czech naming guidelines propose the use of modern Czech orthography for all Last Name at Birth fields for Czech names. Since modern Czech orthography is a relatively recent creation (around 1850 for many Czech regions), this does create issues for names from older records which follow older orthography rules, particularly for the advice to add -ová to female names.
Example 1: For general naming conventions the guide proposes to use the modern version Dvořák and Dvořáková. In older records this name will appear as Dwořak/Dwořakowa, Dworzak/Dworzakowa, or Dworschak. There are numerous people living in Germany, Austria, and the USA who use the name Dworzak or Dworschak today, for example Thomas Dworzak or Leo Ferdinand Dworschak. It does not make sense to me to change their ancestors' name to the modern writing as soon as we are back in Bohemia time wise.
Example 2: Somebody finds Anna Dworzak in a birth register. Not being familiar with Czech orthography but following the style guide he/she changes the name to the female form Dworzaková, thereby creating a chimera of old and new that doesn't really help anybody avoiding to create duplicates, just one more name variation to search for.
In my opinion we should have a pre-1850 and post-1850 version of the naming guidelines to avoid these issues.