Perhaps, perhaps not... The Ferengi long range transporter from "Bloodlines" or "Firstborn" (I can never remember which is which) was specifically said to be a subspace transporter, and transporting of matter through subspace was said to be an unstable endeavor, all this heavily suggesting that the regular deal makes do with ordinary EM or whatnot. But then again, perhaps long range transport always requires subspace versus EM, even when done with Dominion hardware?
That would certainly make sense, as a non-subspace transporter could be expected to be limited to lightspeed. Not only would an interstellar trip take years, those years would be spent in a transporter beam that might begin to degrade within the first few minutes already.
There's some doubt whether Dukat really had a long range transporter in the first place, of course. In "Covenant", the existence of the device is just speculation on the part of our ill-informed heroes (where would Worf get such information, really?). Dukat's disciple doesn't say anything beyond the fact that the transponder was key to bringing Kira to Empok Nor; for all we know, it simply allowed the disciples to beam Kira off the station to a nearby innocent-looking freighter which then relayed the anesthesized victim forth, until a final vessel docked with Empok Nor.
A number of VOY species came up with "space tunnels" of temporary or semi-permanent nature. At least the Waadvaur ones, of the latter type from "Dragon's Teeth", sounded like they weren't related to warp drive in any way. The Federation might construct something like that, but probably only with extreme effort and with all sorts of limitations...
Timo Saloniemi