So after facing the same issue, I came up with a solution. It's not pretty nor elegant, but it works. (At least on my machine)
I just split the logic into 3 different statements. First, I add an empty configSections at the correct position (first). Then I insert the new config to the last configSections, which would be the new one if it is the only one, or a previously existing one otherwise. Lastly I remove any empty configSections elemnt which might exist. I'm using RemoveAll for no good reason, you should probably use Remove.
The overall code looks like so:
<configSections xdt:Transform="InsertBefore(/configuration/*[1])" />
<configSections xdt:Locator="XPath(/configuration/configSections[last()])">
<section name="initialSection" xdt:Locator="Match(name)" xdt:Transform="InsertIfMissing" />
</configSections>
<configSections xdt:Transform="RemoveAll" xdt:Locator="Condition(count(*)=0)" />
The question which still remains unanswered is why Locator conditions are not taken into account for InsertBefore. Or why I can't handle an empty match set for InsertBefore, because that would allowed me to do fun things such as
//configuration/*[position()=1 and not(local-name()='configSections')]
Which to be honest is a much clearer way of doing what I want to achieve.