NGINX Access Log by Location

This is happening because the location that ultimately ends up handling your requests is location ~ \.php$, which inherits its log configuration from the server context. Assuming that the yoast seo sitemap belongs to app1, you'll want a config something like this:

# Use an upstream to future changes easier
upstream _php {
    server unix:/var/run/php/php7.0-fpm.sock;
}

server {
    listen 80 default;
    listen [::]:80;

    root /var/www/html/app1;
    index index.php;

    server_name localhost;

    access_log /var/log/nginx/app1.access.log;
    error_log /var/log/nginx/app1.error.log;    

    # Put php directives in the server context so they can be inherited by all locations
    include fastcgi_params;
    fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;

    location = /favicon.ico { log_not_found off; access_log off; }
    location = /robots.txt { log_not_found off; access_log off; allow all; }

    # Locations that aren't logged can be left outside and shared
    location ~ /\.(?!well-known) {
        deny all;
        access_log off;
        log_not_found off;
    }

    location ~* \.(woff|jpg|jpeg|png|gif|ico|css|js)$ {
        access_log off;
        log_not_found off;
        expires 365d;
    }

    # Everything that logs to app1 should go in here
    location / {
        try_files $uri $uri/ /index.php?$is_args$args;

        # SECURITY : Deny all attempts to access PHP Files in the uploads directory
        location ~* /(?:uploads|files)/.*\.php$ {
            deny all;
        }

        # PHP : pass the PHP scripts to FastCGI server defined in upstream _php
        location ~ \.php$ {
            fastcgi_pass _php;
        }

        # Yoast SEO Sitemaps
        location ~ ([^/]*)sitemap-rewrite-disabled(.*).x(m|s)l$ {
                ## this redirects sitemap.xml to /sitemap_index.xml
            rewrite ^/sitemap.xml$ /sitemap_index.xml permanent;
                ## this makes the XML sitemaps work
                rewrite ^/([a-z]+)?-?sitemap.xsl$ /index.php?xsl=$1 last;
            rewrite ^/sitemap_index.xml$ /index.php?sitemap=1 last;
            rewrite ^/([^/]+?)-sitemap([0-9]+)?.xml$ /index.php?sitemap=$1&sitemap_n=$2 last;
                ## The following lines are optional for the premium extensions
            ## News SEO
                rewrite ^/news-sitemap.xml$ /index.php?sitemap=wpseo_news last;
            ## Local SEO
            rewrite ^/locations.kml$ /index.php?sitemap=wpseo_local_kml last;
            rewrite ^/geo-sitemap.xml$ /index.php?sitemap=wpseo_local last;
            ## Video SEO
            rewrite ^/video-sitemap.xsl$ /index.php?xsl=video last;
        }
    }   

    # Everything that logs to app2 should go in here
    location /app2 {
        try_files $uri $uri/ /app2/index.php$is_args$args;

        access_log /var/log/nginx/app2.access.log;
        error_log  /var/log/nginx/app2.error.log;

        # SECURITY : Deny all attempts to access PHP Files in the uploads directory
        location ~* /(?:uploads|files)/.*\.php$ {
            deny all;
        }

        # PHP : pass the PHP scripts to FastCGI server defined in upstream _php
        location ~ \.php$ {
            fastcgi_pass _php;
        }
    }
}

Moving the fastcgi params into the server and using an upstream for the php server means it's not a lot to duplicate.