Which is the preferred way to configure FPGA in Cyclone V SoC?

Hi,

1) Is there a preferred way out of these two? and why?

In our design example mostly the FPGA is configured during Uboot, but other methods works as well.

2) To be specific does configuring FPGA from Linux has any specific disadvantages? We prefer configuration from Linux, in order to not play with Uboot environment.

This depends on customer design and usage, sometime users want to have access to SDRAM and other FPGA IO or features that they have used in their design that is needed in early phases.

3) Is enabling/disabling bridges by writing to brgmodrst from Linux perfectly normal?

Typically, bridge is enable in Uboot environment, using the Uboot script "run bridge_enable_handoff".

I hope this answers all your questions.