Tonearm relative to Plinth alignment

I have a Linn Basik turntable with a Linn Basik Plus tonearm (bought separately), and when the tonearm is in its arm rest it is not completely parallel with the side of the turntable. It appears to be a few degrees on its way to the platter. There are 3 holes in the table for the screws to the base of the tonearm, and they must be rotated a little bit.

Will this affect the sound of the turntable?

I'm not sure I follow you - are you thinking that loosening the 3 screws may allow the arm to rotate back to its parallel position? Another option may be the VTA set screw. I'm not familiar with the Basic, but my Ittok has a single set screw on the collar - and when you loosen it you can adjust the vertical alignment and also rotate the arm.
No, there are 3 set screws so when they are screwed in, even loosely, you can't rotate it. Here is a picture so you can see:

There would be no way to get it straight short of drilling new holes, so I was wondering if having it start at a few degrees rotation would affect the sound.
As long as your cartridge (cantilever) is properly aligned using a protractor suitable for the tonearm, this shouldn't affect the sound.
I'll defer to Doug's view on the effect, but I still think you can straighten it by rotating the arm in its pivot. If you look at this picture, you can see one set screw that fits horizontally into the pivot plate (ie the round plate that fastens to the plinth). If you loosen it with a hex key you the arm will become free so you can adjust the vertical alignment as well as the alignment to the plinth. Finally - forgive me for stating the obvious - be very careful of your stylus is you loosen this set screw. You may want to prop up the arm with something so the vertical position can't drop.

This is how Linn arms adjust VTA. If it were me, I'd straigten it, though I would not redrill the mounting holes.
The only relevant parameter in locating the tonearm on the plinth, is the distance from spindle-center to tonearm-center. At the correct distance, the tonearm can be located anywhere around spindle. If the tonearm is not parallel with the edge of the plinth when at rest(and this bothers you) then move the tonearm rest so that the arc of the tonearm when it's at rest stops so that the arm is parallel.
I agree with Bdgregory. If you can rotate the arm without changing the distance from pivot-center to spindle-center, that would work. But it is only an aesthetic issue! The outer edge of the plinth could be cut at any angle and this would not affect the turntable's function (e.g., the edges of the "box" could be cut to make a triangle, or a cirlce if that were aethetically sought).
Bdgregory, on the basic plus tonearm, there is a slot on the cylinder that only allow you to adjust the height, but one can not rotate it, so alignment to plinth can not be adjusted
on the basic plus tonearm, there is a slot on the cylinder that only allow you to adjust the height, but one can not rotate it, so alignment to plinth can not be adjusted
now I see . . . this is different than the Linn Ittok, and Audioquest PT6 I previously owned. With those it's very easy to create this alignment issue(which I have done when not paying attention). As noted, it's aesthetics, not function, so if there isn't an easy solution then leave it alone.
Thanks for your responses, everyone.

Dear Dusty: Like every one told you: If the overhang don't change then you don't have any trouble about, my only complaint is about the skating function because some tonearms has this function in a way that the antiskate grow-up all the way LP surface ( increment/higher at the inside grooves ) and the tonearm has to be a initial position ( outside groove ) where the AS is 0 ( cero ), if this is the case with your tonearm then you have to change the position for in the very outside record groove the AS measure cero.

Regards and enjoy the music.

Hello Dusty, if you loosen the 3 bolts underneath there is a little bit of play to rotate it a bit for a slight amount of correction. The arm you have has a groove cut in the pillar so you cannot rotate the arm to swivel it to align.