A few of your questions relate to general power electronics design approaches, which are best discussed with your colleagues although I’d be curious to hear if anyone else on the forum can provide their insights on state of the art practices. I can address your question related to PLECS.
Could anyone share an example or advice on how to implement variable-frequency control for SPS in PLECS?
PLECS has Variable Phase PWM and Variable Frequency PWM modulators built into the component library. For simultaneous control of both variables, I would recommend using one of the modulators from the TI C2000 or STM32 Target Support Library, as described in this forum post. You can also try to build your own modulator out of fundamental components if you need more flexibility. See post 1
and post 2 for ideas.