Is it ok if reconfig_clk (mgmt_clk) is stopped at device startup on Stratix® 10?

Yes, no problem.
Calibration during power-up requires OSC_CLK_1 and all reference clocks supplied to the Transceiver PLL.
It is not necessary to supply reconfig_clk (mgmt_clk) at startup.
However, reconfig_reset (mgmt_reset) should be asserted until reconfig_clk is stably supplied.

--------------------
Category: Transceivers
Tools:-
Device: ^Stratix® 10