Customize Tax amount in "woocommerce_package_rates" hook

Update: related to tax cost calculation for the shipping methods

There is some little errors on your code and you have missed the tax calculation discount. I have revisited your code a bit, you should try this:

add_filter( 'woocommerce_package_rates', 'conditional_shipping_discount', 10, 2 );function conditional_shipping_discount( $rates, $packages ) {    $user_id = get_current_user_id();    if ( ! wc_memberships_is_user_active_member( $user_id, 'silver' ) ) return $rates;    $percent = 30; // 30%    $discount = 1 - ($percent / 100);    foreach($rates as $rate_key => $rate_values ) {        // Get original cost        $original_cost = $rates[$rate_id]->cost;        // Calculate the discounted rate cost        $new_cost = $original_cost * $discount;        // Set the discounted rate cost        $rates[$rate_key]->cost = number_format(new_cost, 2);        // calculate the conversion rate (for taxes)        $conversion_rate = $new_cost / $original_cost;        // Taxes rate cost (if enabled)        $taxes = array();        foreach ($rate->taxes as $key => $tax){            if( $tax > 0 ){ // set the new tax cost                // set the new line tax cost in the taxes array                $taxes[$key] = number_format( $tax * $conversion_rate, 2 );            }        }        // Set the new taxes costs        $rates[$rate_key]->taxes = $taxes    }    return $rates;}

Code goes in function.php file of your active child theme (or theme) or also in any plugin file.

This code is tested and works.

You should need to refresh the shipping caches:

1. First this code is already saved on your function.php file.
   
2. In Shipping settings, enter in a Shipping Zone and disable a Shipping Method and "save". Then re-enable that Shipping Method and "save". You are done.
   

Below code @LoicTheAztec without mistakes:

add_filter( 'woocommerce_package_rates', 'conditional_shipping_discount', 10, 2 );    function conditional_shipping_discount( $rates, $packages ) {    $user_id = get_current_user_id();    if ( ! wc_memberships_is_user_active_member( $user_id, 'silver' ) ) return $rates;    $percent = 30; // 30%    $discount = 1 - ($percent / 100);    foreach($rates as $rate_key => $rate_values ) {        // Get original cost        $original_cost = $rates[$rate_key]->cost;        // Calculate the discounted rate cost        $new_cost = $original_cost * $discount;        // Set the discounted rate cost        $rates[$rate_key]->cost = number_format($new_cost, 2);        // calculate the conversion rate (for taxes)        $conversion_rate = $new_cost / $original_cost;        // Taxes rate cost (if enabled)        $taxes = array();        foreach ($rates[$rate_key]->taxes as $key => $tax){            if( $tax > 0 ){ // set the new tax cost                // set the new line tax cost in the taxes array                $taxes[$key] = number_format( $tax * $conversion_rate, 2 );            }        }        // Set the new taxes costs        $rates[$rate_key]->taxes = $taxes;    }    return $rates;}