The problem occurs in the Calcite Panel component rendered on the popup, and the scrollbar appears as a result of the "content-wrapper" class, which is defined this way: .content-wrapper{overflow:auto}
I've found that adding a bottom padding of 3px to the class definition prevents the scrollbar from appearing unnecessarily. However, since the panel is rendered within a shadow DOM, altering its style is not a simple matter of just overriding the class definition within a style tag.
If you're using a local copy of the API, and loading modules via AMD, you can make the following change in esri/chunks/Panel.js:
Search for: .content-wrapper{overflow:auto}
Replace with: .content-wrapper{overflow:auto;padding-bottom:3px}
If that's not an option, a much uglier hack is to alter the style definition at runtime. Just add the following near where your application starts up:
require(["esri/chunks/panel"], (panel) => {
Object.defineProperty(panel.Panel, "style", {get:function(){return "@keyframes in{0%{opacity:0}100%{opacity:1}}@keyframes in-down{0%{opacity:0;transform:translate3D(0, -5px, 0)}100%{opacity:1;transform:translate3D(0, 0, 0)}}@keyframes in-up{0%{opacity:0;transform:translate3D(0, 5px, 0)}100%{opacity:1;transform:translate3D(0, 0, 0)}}@keyframes in-right{0%{opacity:0;transform:translate3D(-5px, 0, 0)}100%{opacity:1;transform:translate3D(0, 0, 0)}}@keyframes in-left{0%{opacity:0;transform:translate3D(5px, 0, 0)}100%{opacity:1;transform:translate3D(0, 0, 0)}}@keyframes in-scale{0%{opacity:0;transform:scale3D(0.95, 0.95, 1)}100%{opacity:1;transform:scale3D(1, 1, 1)}}:root{--calcite-animation-timing:calc(150ms * var(--calcite-internal-duration-factor));--calcite-internal-duration-factor:var(--calcite-duration-factor, 1);--calcite-internal-animation-timing-fast:calc(100ms * var(--calcite-internal-duration-factor));--calcite-internal-animation-timing-medium:calc(200ms * var(--calcite-internal-duration-factor));--calcite-internal-animation-timing-slow:calc(300ms * var(--calcite-internal-duration-factor))}.calcite-animate{opacity:0;animation-fill-mode:both;animation-duration:var(--calcite-animation-timing)}.calcite-animate__in{animation-name:in}.calcite-animate__in-down{animation-name:in-down}.calcite-animate__in-up{animation-name:in-up}.calcite-animate__in-right{animation-name:in-right}.calcite-animate__in-left{animation-name:in-left}.calcite-animate__in-scale{animation-name:in-scale}@media (prefers-reduced-motion: reduce){:root{--calcite-internal-duration-factor:0.01}}:host{box-sizing:border-box;background-color:var(--calcite-ui-foreground-1);color:var(--calcite-ui-text-2);font-size:var(--calcite-font-size--1)}:host *{box-sizing:border-box}:root{--calcite-floating-ui-transition:var(--calcite-animation-timing);--calcite-floating-ui-z-index:var(--calcite-app-z-index-dropdown)}:host([hidden]){display:none}:host([disabled]){cursor:default;-webkit-user-select:none;user-select:none;opacity:var(--calcite-ui-opacity-disabled)}:host([disabled]) *,:host([disabled]) ::slotted(*){pointer-events:none}:host{position:relative;display:flex;block-size:100%;inline-size:100%;flex:1 1 auto;overflow:hidden;--calcite-min-header-height:calc(var(--calcite-icon-size) * 3);--calcite-panel-footer-padding:0.5rem}:host([disabled]) ::slotted([calcite-hydrated][disabled]),:host([disabled]) [calcite-hydrated][disabled]{opacity:1}.header{margin:0px;display:flex;align-content:space-between;align-items:center;fill:var(--calcite-ui-text-2);color:var(--calcite-ui-text-2)}.heading{margin:0px;padding:0px;font-weight:var(--calcite-font-weight-medium)}.header .heading{flex:1 1 auto;padding:0.5rem}.container{margin:0px;display:flex;inline-size:100%;flex:1 1 auto;flex-direction:column;align-items:stretch;background-color:var(--calcite-ui-background);padding:0px;transition:max-block-size var(--calcite-animation-timing), inline-size var(--calcite-animation-timing)}.container[hidden]{display:none}.header{border-block-end:1px solid;z-index:var(--calcite-app-z-index-header);inline-size:100%;align-items:stretch;justify-content:flex-start;background-color:var(--calcite-ui-foreground-1);border-block-end-color:var(--calcite-ui-border-3);flex:0 0 auto}.action-bar-container{border-block-end:1px solid;z-index:var(--calcite-app-z-index-header);inline-size:100%;border-block-end-color:var(--calcite-ui-border-3)}.action-bar-container ::slotted(calcite-action-bar){inline-size:100%}.header-content{display:flex;flex-direction:column;overflow:hidden;padding-inline:0.75rem;padding-block:0.875rem;margin-inline-end:auto}.header-content .heading,.header-content .description{display:block;overflow-wrap:break-word;padding:0px}.header-content .heading{margin-inline:0px;margin-block:0px 0.25rem;font-size:var(--calcite-font-size-0);line-height:1.25rem;font-weight:var(--calcite-font-weight-medium)}.header-content .heading:only-child{margin-block-end:0px}.header-content .description{font-size:var(--calcite-font-size--1);line-height:1rem;color:var(--calcite-ui-text-2)}.back-button{border-width:0px;border-style:solid;border-color:var(--calcite-ui-border-3);border-inline-end-width:1px}.header-actions{display:flex;flex-direction:row;flex-wrap:nowrap;align-items:stretch}.header-actions--end{margin-inline-start:auto}.content-wrapper{overflow:auto;padding-bottom:3px}.content-height{block-size:100%}.content-container{display:flex;flex:1 1 auto;flex-direction:column;flex-wrap:nowrap;align-items:stretch;background-color:var(--calcite-ui-background)}.footer{border-block-start:1px solid;display:flex;inline-size:100%;justify-content:space-evenly;background-color:var(--calcite-ui-foreground-1);border-block-start-color:var(--calcite-ui-border-3);flex:0 0 auto;padding:var(--calcite-panel-footer-padding)}.fab-container{position:sticky;inset-block-end:0px;z-index:var(--calcite-app-z-index-sticky);margin-block:0px;margin-inline:auto;display:block;padding:0.5rem;inset-inline:0;inline-size:-moz-fit-content;inline-size:fit-content}[hidden]{display:none}";}});
});
(The only effective change is the inclusion of the text ";padding-bottom:3px").
