So these two planets are in the same system....

Just to be sure I understand the effect of tunneled slipgates; does the slipgate effect negate the negative effects of the strong magnetic field?

I would expect yes, except for the disapproval effect, as its not part of the "Set FIDSI penalty to 0". But to be certain you probably have to colonize the system and see how the effects are listed, e.g. how the planet's base output is, compared to a planet of same type without the negative anomaly. (This could be found ingame or in tables such as here)