How should my fiancée and I, residing in different countries, apply for Schengen visas separately or together?

My fiancée and I, both Indian citizens, are planning to get married in December, followed by a honeymoon trip to a few places in Europe (Amsterdam, Helsinki, Paris). I reside and work in Japan (since about three years ago), while she resides and works in India. I have a monthly income of around ¥350000 (~€3000), and her monthly income is around INR 40000 (~€500). The trip will largely be paid for by me (flight and hotel bookings).

I understand that the usual advice here is for both of us to apply together. However, I won't be returning to India until just before the wedding, so it's not practical for me to apply in India (assuming I might have to personally go to an embassy or consulate).

How should we apply here? If we apply separately (in India and Japan respectively), should we provide a statement that we will be getting married, and provide both our financial documents with both applications?

An update:

I applied to the Dutch embassy in Tokyo, using only my own financial documents. I stated in the cover letter (twice, both at the start and at the end) that I'll be supporting both of us during the trip. However, the official who collected the application and documents did not ask me anything about that (I was congratulated about the wedding, so I think they did note it). The only questions were:

• about the stay for a night for which I hadn't mentioned hotel bookings (we had an overnight flight with a connection, so we would stay in the airport)
• about my travel between Japan and India (then I submitted the ticket for those flights)

The visa was approved in one week. Now we will proceed with my fiancée's application.

Final update: my fiancée's visa application was denied a couple of weeks ago. The reasons included:

I think the refusal might be due to the following reasons:

• My fiancée had already submitted her resignation at her job, since she will be visiting Japan after the honeymoon (she had already obtained a Japanese short-term visitor visa prior to applying for the Schengen visa). I suppose that as a single, unemployed person with not much in the way of personal possessions, she is now prime illegal immigration risk.
• The hotel reservations from booking.com were all in my name (since best I can tell, booking.com only puts the primary guest's name in the confirmation). I had provided a signed letter stating that the reservations were all for two people, and that she would be staying with me, but I suppose it was insufficient.

The denial came a week after she had applied. At this stage, we aren't going to appeal - the communication address is in Netherlands and not our local consulate, so the time taken in international mail communication alone would mean the process and any back-and-forth could take more time than we have.