In my honest opinion -12dB tone for allignment seems too high for me assuming that nominal programme level will be around this tone level. If the original -12dBFS tone was passed to DigiBeta without analog conversion it should have mantained these level to DigiBeta. Common allignment levels (and nominal programme levels) for DigiBeta are -20dBFS (SMPTE) or -18dBFS (EBU). Not sure but it sounds like they were asking to you a "NLE" signal level that, when passed to a DigiBeta recorder resulted too hot.
When NLE and non-betacam cameras came into play we had to talk with editors in order to keep our levels the same. For example, Final Cut Tones were by defect at -12dBsFS and this was the nominal programme level editors used, so their work used to sound hot when going to transfer to Digibeta.
In my experience I´ve found 2 kind of problems regarding levels (3 if you have both them):
signal mantains digital from source to destiny. Recommended allignment levels for digital interexchange of material can vary from USA to Europe, for example, but it is easy to find out wich standard has been followed just by checking tones.
signal is converted digital to analog or viceversa in some stage. There are 2 main recommendations for analog to digital conversion values so the allignment issue can be tricky in this case. For example, a -12dBFS tone is recorded in a SMPTE DigiBeta VTR, then its analog outputs are connected to analog inputs of an "EBU adjusted" VTR recorder. The second one will meter -6dBFS. Of course, it is not your case.
Anyway, both of this main recommended allignment levels are near each other (-20 and -18dBFS) so -12dB would be too high for each of them.
We have had some level issues in the last years since part of our signal chain was analog and the other was digital; some of our equipment was analog and some digital.
For international material exchange I´d recommend reading:
For analog to digital conversion levels:
My English is not as good as my Basque or Spanish, but I hope this helps.