In our opinion, it is always best to have a dialog with a sales rep at the factory for the best support on the PCB / PCBA quoting. There are just too many variables that can break the quote if the online software is not fully baked. The sales staff will know their capabilities much better than perhaps the quoting system can convey.
As an example, Kingford can support via in pad as a normal process and had the best offer for a recent design with WLCSP packages (0.4mm ball pitch) yet other shops in China are charging multiple times the quote as they consider the design to be HDI density. Let alone, North America vendors are charging even higher.
In another thread on this forum, we faced some issues with JLCPCB - the summary of this experience is, if the design fits their capabilities, then JLCPCB is hard to beat on the price and lead times. Pay some more and you can work with a shop like Kingford, Yaxinda, Suntak, Fast Turn PCB, China Fast Print, etc. and they will just get the job done.