Advanced Permissions is still the way to restrict blocks in an area.

Can you explain a little more about your second question, not sure what you are asking.

1) When I do this, I loose ability to edit the block.

$nav = BlockType::getByHandle('autonav');
$nav->controller->orderBy = 'display_asc';
$nav->controller->displayPages = 'top';
$nav->controller->displaySubPages = 'all';
$nav->controller->displaySubPageLevels = 'custom';
$nav->controller->displaySubPageLevelsNum = 1;
$nav->render('view');

Is there some param, to make it editable?

2) Can you please give small step by step, how to limit those blocks for areas with permissions? I can't find these stuff.

1) If you "hard code" a block into your template, it will not be editable, which is what you are doing by doing it this way. If you want the block to be editable you have to add it into an area as you normally would.

2) Take a look at the last post on this thread for instructions -https://www.concrete5.org/community/forums/customizing_c5/restrictin...

1) Put a page in Edit mode
2) Click on 'Add to Main' (or whatever area you want to restrict)
3) Then choose 'Set Permissions'.

This Fails, as there is no Set permissions in drop-down. Advanced mode is oN.

What version are you using? This shows up for me with the newest 5.7 version, it's just called "Permissions" but it's there.

8.1.0, the one in download page

For some reason, permissions are not there fro "GlobalArea". For new Area works.

For the Global Area try going to the Dashboard -> Stacks & Blocks -> Stacks -> Global Areas and see if it's there.

Kind of isn't, only for the block set inside :D.. I will research more on Stacks.