Frankly, it is not realistic to expect FastMail to stop developing the current interface in case it causes unsupported Stylish scripts to be affected. As a practical matter, most tweaks will probably continue to work (as did the CSS tweaks in the classic interface) but occasional upwards compatibility issues should be expected.
For that reason, it is probably prudent to restrict use of such tweaks to situations where it really makes a significant difference to your FastMail experience.
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