It is just a transliteration preference. The Cyrillic character Tse (Ц) does not have an exact opposite sound in English, French, German, etc., so depending on your transliteration approach it can either be done as "Cz," "Ts," or "Tz" to approximate the same sound. For an English speaker it is like the "zz" in "pizza" — a sort of quick t and z combination. Depending on which transliteration scheme you use, it might be transliterated as "c", "z", or "tc" as well.

I don't think it signifies any deep shift in historians' understanding. Transliteration is somewhat arbitrary. Preferred schemes come and go. Some transliteration schemes are strongly influenced by the underlying language that is being transliterated into, so if the person coming up with the Cyrillic to Roman scheme was English, German, or French, they might each regard certain sequences a better fit. One sees this especially with the "j" character which has a very different sound in German than it does in English (the Cyrillic "Я" is transliterated as "Ya" in English but "Ja" in German). The German "c" sound can be quite "soft" (like "Celsius"), so it may be the "Czar" is derived from a German transliteration; I don't know.

As for usage patterns — one might ask at /r/asklinguistics but my understanding is that in the late 20th century, there was some sort of general shift in the academy away from some transliterations to others. "Tsar" is the common way that it is taught in Russian classes today. One can use something like Google Ngrams to chart the changing frequency of some common transliterations over time — it seems to show that "Czar" was far more common prior to 1920, at which point "Tsar" started to take over. In the present period, "czar" holds about 35% of the "real estate" in English-language books, whereas "tsar" holds about 64%. If you capitalize them you get slightly better odds for "Czar", and the crossover point changes (perhaps more auspiciously) to 1914. (Switching the language to German gives interesting results — a total riot prior to 1960, at which point it becomes standardized as "tsar".)

Again, I don't think this reflects anything too deep about scholarly understanding. At most, I suspect, it reflects a shifting attention to Russia given in English-speaking contexts — if the other transliteration was borrowed from German-speaking authors, and reflects German phonemes, then increased interest in Russia (as occurred around and after the WWI period) may have caused a more comprehensive transliteration reform in the UK/US contexts, which eventually dribbled down to popular spellings. But this is speculation on my part.