I realize doxycycline for 2 weeks 2x100mg/day can treat primary syphilis. but what about incubating syphilis (before any symptoms present)? could starting 10 days of doxycycline (2x100mg/day) within 24-48hrs post exposure prevent infection?

Yes. Doxycycline is equally effective in preventing syphilis as it is in treating an established infection. In fact, for prevention 7 days of doxycycline is sufficient.

Incubation period is the time before symptoms occur. Antibiotics kill the bacteria causing the disease when manifest and if taken after exposure- in the incubating stage. So yes- it will prevent it