I suppose you could use rod magnets? They would sit flush with the bottom of the bases, and positioned carefully, could stand proud of the base tops and be used as pins to secure the miniature to the base.
So for example, if you're using 1.5mm thick bases, you could use some
2 x 8mm magnets, which would leave you 6.5mm to "pin" the model's feet onto the base top.
This would also have the advantage that as well as a strong bond between the model and the base, the model itself "hides" the magnets from view. For an average 25mm human model, a 130g pull on each foot should be enough to keep them securely magnetised to your transport tray of choice.
The biggest downsides I see are: figures with small feet (you may need to glue these on as normal, and then drill a shallow magnet into the base underneath - some grey paint in the hole first, and it should be discreet if still a little visible), and big figures that may need bigger rods in order to get enough "pull" to secure them. Also, models which are fairly unbalanced and are offset on the base will have the magnets positioned rather eccentrically on the base, which may cause movement during transport. If you use smaller models, or stick to lighter plastic/resin figures, these things are much less of an issue (even though they still require some consideration as I've explained).
Anyway, that's just an idea I came up a good while back when I considered using magnets for the same basing style. Hope it helps you!
