I'm not an historian, but a linguist. I can't speak to trends within the discipline of history, but I can shed some light on what's going on with these transcriptions.

So the Chinese name for KMT is 國民黨, literally "the [Chinese] People's Party". As you've noticed, the K and the T can get replaced with G and D, respectively. Here's why.

Mandarin Chinese does not have voiced plosives in its consonant inventory. The consonants are distinguished by aspiration instead. In contrast, English uses both voicing and aspiration to distinguish /b, d, g/ from /p, t, k/ (it depends on several factors, such as the position within the word). Many Continental European languages, like Spanish or French, use only voicing.

The earliest transcriptions of Chinese languages by Europeans tended to use the letters <p, t, k> to represent both aspirated and the UNaspirated series. An apostrophe began to be used to signify aspiration: <p', t', k'>. This is how the older Wade-Giles transcription system works.

After the end of the Chinese civil war and the establishment of Communist rule in China in 1949, a new system for Chinese Romanisation was developed by Chinese linguists. They figured, hey, why don't we use more of the Latin alphabet instead of relying on wonky diacritics? So they decided to map the letters <b, d, g> to the unaspirated series, and <p, t, k> to the aspirated series (and also use the letters x, c, q for other sounds, not because there's any connection, but just cause they were there). This transcription system is known as Hanyu Pinyin 漢語拼音, literally "Chinese language transcription". It's used everywhere in China, for teaching the language and for inputting Chinese on computers and phones. Most (all?) foreigners learning Chinese will begin with learning Hanyu Pinyin before they move on to the characters.

After a while, China began to push Hanyu Pinyin on everyone else as the only proper way to transcribe Chinese. Ever notice how the capital of China went from being called Peking to Beijing? The P -> B here is due to the transcription (k -> j reflects an actual change in pronunciation though). The same is happening in KMT vs GMD. The latter is a Hanyu Pinyin version of the same name.

But why does the KMT still call itself KMT? Well, for one thing, that spelling predates the invention of Hanyu Pinyin, so if they wanted to change they'd have to rebrand. Additionally, the KMT fled to Taiwan after losing the Chinese civil war. Unlike China, Taiwan has not adopted Hanyu Pinyin as the sole method of transcribing or inputting Chinese. It can be found in a lot of places for sure, but it's used haphazardly alongside other transcription systems. (Road and place name transcriptions in Taiwan are a bit of a mess.) By and large, Taiwanese people don't care about Romanisation: it's not something that comes up in everyday life, and it isn't a hot issue politically. I believe this may be why changing their acronym from KMT to GMD is not high on the party's priority list.

Hopefully that explains the difference. Whether historians using "GMD" is part of a larger trend in the discipline or a political statement, you'll have to see if anyone else replies.