from reading pcsx-rearmed code i learn that we can write to pcsx.cfg (should be placed near pcsx in hidden derectory(appear after first run) ) next variables
Bios,Gpu,Spu,Cdr - string type
scaling,g_layer_x,g_layer_y,g_layer_w,g_layer_h,fi lter,state_slot,cpu_clock,g_opts,iUseDither, UseFrameSkip,UseFrameLimit,dwActFixes,iUseReverb, iUseInterpolation, iXAPitch,iSPUIRQWait,iUseTimer - boolean type (0 or 1)
so you can try to run pcsx with other GPU and enable framiskiping
i grant no guarantee to this